Loading...
Sign in to edit your profile (add interests, mentoring, photo, etc.)

    Adam Godzik

    TitleDirector
    SchoolUniversity of California, San Diego
    DepartmentCenter for Research in Biological Systems
    Address9500 Gilman Drive #0608
    CA La Jolla 92093
    vCardDownload vCard

      Collapse Bibliographic 
      Collapse Publications
      Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
      List All   |   Timeline
      1. Climente-González H, Porta-Pardo E, Godzik A, Eyras E. The Functional Impact of Alternative Splicing in Cancer. Cell Rep. 2017 Aug 29; 20(9):2215-2226. PMID: 28854369.
        View in: PubMed
      2. Porta-Pardo E, Kamburov A, Tamborero D, Pons T, Grases D, Valencia A, Lopez-Bigas N, Getz G, Godzik A. Comparison of algorithms for the detection of cancer drivers at subgene resolution. Nat Methods. 2017 Aug; 14(8):782-788. PMID: 28714987.
        View in: PubMed
      3. Derewenda ZS, Godzik A. The "Sticky Patch" Model of Crystallization and Modification of Proteins for Enhanced Crystallizability. Methods Mol Biol. 2017; 1607:77-115. PMID: 28573570.
        View in: PubMed
      4. Porta-Pardo E, Godzik A. Mutation Drivers of Immunological Responses to Cancer. Cancer Immunol Res. 2016 Sep 02; 4(9):789-98. PMID: 27401919.
        View in: PubMed
      5. Braten O, Livneh I, Ziv T, Admon A, Kehat I, Caspi LH, Gonen H, Bercovich B, Godzik A, Jahandideh S, Jaroszewski L, Sommer T, Kwon YT, Guharoy M, Tompa P, Ciechanover A. Numerous proteins with unique characteristics are degraded by the 26S proteasome following monoubiquitination. Proc Natl Acad Sci U S A. 2016 Aug 9; 113(32):E4639-47. PMID: 27385826; PMCID: PMC4987823 [Available on 02/09/17].
      6. Moldt B, Le KM, Carnathan DG, Whitney JB, Schultz N, Lewis MG, Borducchi EN, Smith KM, Mackel JJ, Sweat SL, Hodges AP, Godzik A, Parren PW, Silvestri G, Barouch DH, Burton DR. Neutralizing antibody affords comparable protection against vaginal and rectal simian/human immunodeficiency virus challenge in macaques. AIDS. 2016 Jun 19; 30(10):1543-51. PMID: 27243773; PMCID: PMC4915739 [Available on 06/19/17].
      7. Serrano P, Dutta SK, Proudfoot A, Mohanty B, Susac L, Martin B, Geralt M, Jaroszewski L, Godzik A, Elsliger M, Wilson IA, Wüthrich K. NMR in structural genomics to increase structural coverage of the protein universe: Delivered by Prof. Kurt Wüthrich on 7 July 2013 at the 38th FEBS Congress in St. Petersburg, Russia. FEBS J. 2016 Nov; 283(21):3870-3881. PMID: 27154589.
        View in: PubMed
      8. Xu Q, Shoji M, Shibata S, Naito M, Sato K, Elsliger MA, Grant JC, Axelrod HL, Chiu HJ, Farr CL, Jaroszewski L, Knuth MW, Deacon AM, Godzik A, Lesley SA, Curtis MA, Nakayama K, Wilson IA. A Distinct Type of Pilus from the Human Microbiome. Cell. 2016 Apr 21; 165(3):690-703. PMID: 27062925; NIHMSID: NIHMS769124 [Available on 04/21/17].
        View in: PubMed
      9. Stepanyuk GA, Serrano P, Peralta E, Farr CL, Axelrod HL, Geralt M, Das D, Chiu HJ, Jaroszewski L, Deacon AM, Lesley SA, Elsliger MA, Godzik A, Wilson IA, Wüthrich K, Salomon DR, Williamson JR. UHM-ULM interactions in the RBM39-U2AF65 splicing-factor complex. Acta Crystallogr D Struct Biol. 2016 Apr; 72(Pt 4):497-511. PMID: 27050129; PMCID: PMC4822562 [Available on 03/24/17].
      10. McLuskey K, Grewal JS, Das D, Godzik A, Lesley SA, Deacon AM, Coombs GH, Elsliger MA, Wilson IA, Mottram JC. Crystal Structure and Activity Studies of the C11 Cysteine Peptidase from Parabacteroides merdae in the Human Gut Microbiome. J Biol Chem. 2016 Apr 29; 291(18):9482-91. PMID: 26940874; PMCID: PMC4850288.
      11. Landais E, Huang X, Havenar-Daughton C, Murrell B, Price MA, Wickramasinghe L, Ramos A, Bian CB, Simek M, Allen S, Karita E, Kilembe W, Lakhi S, Inambao M, Kamali A, Sanders EJ, Anzala O, Edward V, Bekker LG, Tang J, Gilmour J, Kosakovsky-Pond SL, Phung P, Wrin T, Crotty S, Godzik A, Poignard P. Broadly Neutralizing Antibody Responses in a Large Longitudinal Sub-Saharan HIV Primary Infection Cohort. PLoS Pathog. 2016 Jan; 12(1):e1005369. PMID: 26766578.
        View in: PubMed
      12. Jahandideh S, Sharifi F, Jaroszewski L, Godzik A. PROPER: Performance visualization for optimizing and comparing ranking classifiers in MATLAB. Source Code Biol Med. 2015; 10:15. PMID: 26635892; PMCID: PMC4668683.
      13. Hrabe T, Li Z, Sedova M, Rotkiewicz P, Jaroszewski L, Godzik A. PDBFlex: exploring flexibility in protein structures. Nucleic Acids Res. 2016 Jan 4; 44(D1):D423-8. PMID: 26615193; PMCID: PMC4702920.
      14. Sedova M, Jaroszewski L, Godzik A. Protael: protein data visualization library for the web. Bioinformatics. 2016 Feb 15; 32(4):602-4. PMID: 26515826.
        View in: PubMed
      15. Porta-Pardo E, Garcia-Alonso L, Hrabe T, Dopazo J, Godzik A. A Pan-Cancer Catalogue of Cancer Driver Protein Interaction Interfaces. PLoS Comput Biol. 2015 Oct; 11(10):e1004518. PMID: 26485003; PMCID: PMC4616621.
      16. Xu Q, Mengin-Lecreulx D, Liu XW, Patin D, Farr CL, Grant JC, Chiu HJ, Jaroszewski L, Knuth MW, Godzik A, Lesley SA, Elsliger MA, Deacon AM, Wilson IA. Insights into Substrate Specificity of NlpC/P60 Cell Wall Hydrolases Containing Bacterial SH3 Domains. MBio. 2015 Sep 15; 6(5):e02327-14. PMID: 26374125; PMCID: PMC4600125.
      17. Dutta SK, Serrano P, Geralt M, Axelrod HL, Xu Q, Lesley SA, Godzik A, Deacon AM, Elsliger MA, Wilson IA, Wüthrich K. Cofactor-induced reversible folding of Flavodoxin-4 from Lactobacillus acidophilus. Protein Sci. 2015 Oct; 24(10):1600-8. PMID: 26177955; PMCID: PMC4594659 [Available on 10/01/16].
      18. Hayashi Y, Caboni L, Das D, Yumoto F, Clayton T, Deller MC, Nguyen P, Farr CL, Chiu HJ, Miller MD, Elsliger MA, Deacon AM, Godzik A, Lesley SA, Tomoda K, Conklin BR, Wilson IA, Yamanaka S, Fletterick RJ. Structure-based discovery of NANOG variant with enhanced properties to promote self-renewal and reprogramming of pluripotent stem cells. Proc Natl Acad Sci U S A. 2015 Apr 14; 112(15):4666-71. PMID: 25825768; PMCID: PMC4403148.
      19. Xu D, Jaroszewski L, Li Z, Godzik A. AIDA: ab initio domain assembly for automated multi-domain protein structure prediction and domain-domain interaction prediction. Bioinformatics. 2015 Jul 1; 31(13):2098-105. PMID: 25701568; PMCID: PMC4481839.
      20. Natarajan P, Punta M, Kumar A, Yeh AP, Godzik A, Aravind L. Structure and sequence analyses of Bacteroides proteins BVU_4064 and BF1687 reveal presence of two novel predominantly-beta domains, predicted to be involved in lipid and cell surface interactions. BMC Bioinformatics. 2015 Jan 16; 16:7. PMID: 25592227; PMCID: PMC4387736.
      21. Porta Pardo E, Godzik A. Analysis of individual protein regions provides novel insights on cancer pharmacogenomics. PLoS Comput Biol. 2015 Jan; 11(1):e1004024. PMID: 25568936; PMCID: PMC4287345.
      22. Xu Q, Mengin-Lecreulx D, Patin D, Grant JC, Chiu HJ, Jaroszewski L, Knuth MW, Godzik A, Lesley SA, Elsliger MA, Deacon AM, Wilson IA. Structure-guided functional characterization of DUF1460 reveals a highly specific NlpC/P60 amidase family. Structure. 2014 Dec 2; 22(12):1799-809. PMID: 25465128; NIHMSID: NIHMS643899.
        View in: PubMed
      23. Porta-Pardo E, Hrabe T, Godzik A. Cancer3D: understanding cancer mutations through protein structures. Nucleic Acids Res. 2015 Jan; 43(Database issue):D968-73. PMID: 25392415; PMCID: PMC4383948.
      24. Chiu HJ, Grant JC, Farr CL, Jaroszewski L, Knuth MW, Miller MD, Elsliger MA, Deacon AM, Godzik A, Lesley SA, Wilson IA. Structural analysis of arabinose-5-phosphate isomerase from Bacteroides fragilis and functional implications. Acta Crystallogr D Biol Crystallogr. 2014 Oct 1; 70(Pt 10):2640-51. PMID: 25286848.
        View in: PubMed
      25. Ratnikov BI, Cieplak P, Gramatikoff K, Pierce J, Eroshkin A, Igarashi Y, Kazanov M, Sun Q, Godzik A, Osterman A, Stec B, Strongin A, Smith JW. Basis for substrate recognition and distinction by matrix metalloproteinases. Proc Natl Acad Sci U S A. 2014 Oct 07; 111(40):E4148-55. PMID: 25246591; PMCID: PMC4210027.
      26. Hwang WC, Golden JW, Pascual J, Xu D, Cheltsov A, Godzik A. Site-specific recombination of nitrogen-fixation genes in cyanobacteria by XisF-XisH-XisI complex: Structures and models. Proteins. 2014 Sep 1. PMID: 25179344.
        View in: PubMed
      27. Zmasek CM, Godzik A. Phylogenomic analysis of glycogen branching and debranching enzymatic duo. BMC Evol Biol. 2014 Aug 23; 14:183. PMID: 25148856; PMCID: PMC4236520.
      28. Kumar A, Punta M, Axelrod HL, Das D, Farr CL, Grant JC, Chiu HJ, Miller MD, Coggill PC, Klock HE, Elsliger MA, Deacon AM, Godzik A, Lesley SA, Wilson IA. Crystal structures of three representatives of a new Pfam family PF14869 (DUF4488) suggest they function in sugar binding/uptake. Protein Sci. 2014 Oct; 23(10):1380-91. PMID: 25044324; PMCID: PMC4287006.
      29. Hwang WC, Xu Q, Wu B, Godzik A. Crystal structure of a Baeyer-Villiger flavin-containing monooxygenase from Staphylococcus aureus MRSA strain MU50. Proteins. 2014 Aug 05. PMID: 25092800.
        View in: PubMed
      30. Porta-Pardo E, Godzik A. e-Driver: a novel method to identify protein regions driving cancer. Bioinformatics. 2014 Nov 01; 30(21):3109-14. PMID: 25064568; PMCID: PMC4609017.
      31. Okamoto S, Nakamura T, Cieplak P, Chan SF, Kalashnikova E, Liao L, Saleem S, Han X, Clemente A, Nutter A, Sances S, Brechtel C, Haus D, Haun F, Sanz-Blasco S, Huang X, Li H, Zaremba JD, Cui J, Gu Z, Nikzad R, Harrop A, McKercher SR, Godzik A, Yates JR, Lipton SA. S-nitrosylation-mediated redox transcriptional switch modulates neurogenesis and neuronal cell death. Cell Rep. 2014 Jul 10; 8(1):217-28. PMID: 25001280.
        View in: PubMed
      32. Jaroszewski L, Koska L, Sedova M, Godzik A. PubServer: literature searches by homology. Nucleic Acids Res. 2014 Jul; 42(Web Server issue):W430-5. PMID: 24957597.
        View in: PubMed
      33. Rigden DJ, Eberhardt RY, Gilbert HJ, Xu Q, Chang Y, Godzik A. Structure- and context-based analysis of the GxGYxYP family reveals a new putative class of glycoside hydrolase. BMC Bioinformatics. 2014 Jun 17; 15:196. PMID: 24938123; PMCID: PMC4071793.
      34. Fleischman NM, Das D, Kumar A, Xu Q, Chiu HJ, Jaroszewski L, Knuth MW, Klock HE, Miller MD, Elsliger MA, Godzik A, Lesley SA, Deacon AM, Wilson IA, Toney MD. Molecular characterization of novel pyridoxal-5'-phosphate-dependent enzymes from the human microbiome. Protein Sci. 2014 Aug; 23(8):1060-76. PMID: 24888348.
        View in: PubMed
      35. Li Z, Natarajan P, Ye Y, Hrabe T, Godzik A. POSA: a user-driven, interactive multiple protein structure alignment server. Nucleic Acids Res. 2014 Jul; 42(Web Server issue):W240-5. PMID: 24838569; PMCID: PMC4086100.
      36. Xu D, Jaroszewski L, Li Z, Godzik A. AIDA: ab initio domain assembly server. Nucleic Acids Res. 2014 Jul; 42(Web Server issue):W308-13. PMID: 24831546.
        View in: PubMed
      37. Hrabe T, Godzik A. ConSole: using modularity of contact maps to locate solenoid domains in protein structures. BMC Bioinformatics. 2014 Apr 27; 15:119. PMID: 24766872; PMCID: PMC4021314.
      38. Sheydina A, Eberhardt RY, Rigden DJ, Chang Y, Li Z, Zmasek CC, Axelrod HL, Godzik A. Structural genomics analysis of uncharacterized protein families overrepresented in human gut bacteria identifies a novel glycoside hydrolase. BMC Bioinformatics. 2014 Apr 17; 15:112. PMID: 24742328; PMCID: PMC4032388.
      39. Das D, Murzin AG, Rawlings ND, Finn RD, Coggill P, Bateman A, Godzik A, Aravind L. Structure and computational analysis of a novel protein with metallopeptidase-like and circularly permuted winged-helix-turn-helix domains reveals a possible role in modified polysaccharide biosynthesis. BMC Bioinformatics. 2014 Mar 19; 15:75. PMID: 24646163; PMCID: PMC4000134.
      40. Jahandideh S, Jaroszewski L, Godzik A. Improving the chances of successful protein structure determination with a random forest classifier. Acta Crystallogr D Biol Crystallogr. 2014 Mar; 70(Pt 3):627-35. PMID: 24598732.
        View in: PubMed
      41. Ravcheev DA, Godzik A, Osterman AL, Rodionov DA. Polysaccharides utilization in human gut bacterium Bacteroides thetaiotaomicron: comparative genomics reconstruction of metabolic and regulatory networks. BMC Genomics. 2013 Dec 12; 14:873. PMID: 24330590; PMCID: PMC3878776.
      42. Hwang WC, Bakolitsa C, Punta M, Coggill PC, Bateman A, Axelrod HL, Rawlings ND, Sedova M, Peterson SN, Eberhardt RY, Aravind L, Pascual J, Godzik A. LUD, a new protein domain associated with lactate utilization. BMC Bioinformatics. 2013 Nov 26; 14:341. PMID: 24274019; PMCID: PMC3924224.
      43. Das D, Chiu HJ, Farr CL, Grant JC, Jaroszewski L, Knuth MW, Miller MD, Tien HJ, Elsliger MA, Deacon AM, Godzik A, Lesley SA, Wilson IA. Crystal structure of a putative quorum sensing-regulated protein (PA3611) from the Pseudomonas-specific DUF4146 family. Proteins. 2014 Jun; 82(6):1086-92. PMID: 24174223.
        View in: PubMed
      44. Eroshkin AM, LeBlanc A, Weekes D, Post K, Li Z, Rajput A, Butera ST, Burton DR, Godzik A. bNAber: database of broadly neutralizing HIV antibodies. Nucleic Acids Res. 2014 Jan; 42(Database issue):D1133-9. PMID: 24214957; PMCID: PMC3964981.
      45. Xu D, Jaroszewski L, Li Z, Godzik A. FFAS-3D: improving fold recognition by including optimized structural features and template re-ranking. Bioinformatics. 2014 Mar 1; 30(5):660-7. PMID: 24130308.
        View in: PubMed
      46. Das D, Hervé M, Elsliger MA, Kadam RU, Grant JC, Chiu HJ, Knuth MW, Klock HE, Miller MD, Godzik A, Lesley SA, Deacon AM, Mengin-Lecreulx D, Wilson IA. Structure and function of a novel LD-carboxypeptidase a involved in peptidoglycan recycling. J Bacteriol. 2013 Dec; 195(24):5555-66. PMID: 24123814; PMCID: PMC3889619.
      47. Bhabha G, Ekiert DC, Jennewein M, Zmasek CM, Tuttle LM, Kroon G, Dyson HJ, Godzik A, Wilson IA, Wright PE. Divergent evolution of protein conformational dynamics in dihydrofolate reductase. Nat Struct Mol Biol. 2013 Nov; 20(11):1243-9. PMID: 24077226; PMCID: PMC3823643.
      48. Xu Q, Chiu HJ, Farr CL, Jaroszewski L, Knuth MW, Miller MD, Lesley SA, Godzik A, Elsliger MA, Deacon AM, Wilson IA. Structures of a Bifunctional Cell Wall Hydrolase CwlT Containing a Novel Bacterial Lysozyme and an NlpC/P60 dl-Endopeptidase. J Mol Biol. 2014 Jan 9; 426(1):169-84. PMID: 24051416.
        View in: PubMed
      49. Xu Q, Grant J, Chiu HJ, Farr CL, Jaroszewski L, Knuth MW, Miller MD, Lesley SA, Godzik A, Elsliger MA, Deacon AM, Wilson IA. Crystal structure of a member of a novel family of dioxygenases (PF10014) reveals a conserved cupin fold and active site. Proteins. 2014 Jan; 82(1):164-70. PMID: 23852666.
        View in: PubMed
      50. Coggill P, Eberhardt RY, Finn RD, Chang Y, Jaroszewski L, Godzik A, Das D, Xu Q, Axelrod HL, Aravind L, Murzin AG, Bateman A. Two Pfam protein families characterized by a crystal structure of protein lpg2210 from Legionella pneumophila. BMC Bioinformatics. 2013; 14:265. PMID: 24004689.
        View in: PubMed
      51. Castellana NE, Lushnikov A, Rotkiewicz P, Sefcovic N, Pevzner PA, Godzik A, Vyatkina K. MORPH-PRO: a novel algorithm and web server for protein morphing. Algorithms Mol Biol. 2013; 8(1):19. PMID: 23844614.
        View in: PubMed
      52. Chang RL, Andrews K, Kim D, Li Z, Godzik A, Palsson BO. Structural systems biology evaluation of metabolic thermotolerance in Escherichia coli. Science. 2013 Jun 7; 340(6137):1220-3. PMID: 23744946.
        View in: PubMed
      53. Das D, Lee WS, Grant JC, Chiu HJ, Farr CL, Vance J, Klock HE, Knuth MW, Miller MD, Elsliger MA, Deacon AM, Godzik A, Lesley SA, Kornfeld S, Wilson IA. Structure and function of the DUF2233 domain in bacteria and in the human mannose 6-phosphate uncovering enzyme. J Biol Chem. 2013 Jun 07; 288(23):16789-99. PMID: 23572527; PMCID: PMC3675612.
      54. Zmasek CM, Godzik A. Evolution of the animal apoptosis network. Cold Spring Harb Perspect Biol. 2013 Mar 01; 5(3):a008649. PMID: 23457257; PMCID: PMC3578353.
      55. Zmasek CM, Godzik A. This Déjà vu feeling--analysis of multidomain protein evolution in eukaryotic genomes. PLoS Comput Biol. 2012; 8(11):e1002701. PMID: 23166479; PMCID: PMC3499355.
      56. Burton DR, Ahmed R, Barouch DH, Butera ST, Crotty S, Godzik A, Kaufmann DE, McElrath MJ, Nussenzweig MC, Pulendran B, Scanlan CN, Schief WR, Silvestri G, Streeck H, Walker BD, Walker LM, Ward AB, Wilson IA, Wyatt R. A Blueprint for HIV Vaccine Discovery. Cell Host Microbe. 2012 Oct 18; 12(4):396-407. PMID: 23084910.
        View in: PubMed
      57. Kumar A, Möcklinghoff S, Yumoto F, Jaroszewski L, Farr CL, Grzechnik A, Nguyen P, Weichenberger CX, Chiu HJ, Klock HE, Elsliger MA, Deacon AM, Godzik A, Lesley SA, Conklin BR, Fletterick RJ, Wilson IA. Structure of a novel winged-helix like domain from human NFRKB protein. PLoS One. 2012; 7(9):e43761. PMID: 22984442.
        View in: PubMed
      58. Xu Q, van Wezel GP, Chiu HJ, Jaroszewski L, Klock HE, Knuth MW, Miller MD, Lesley SA, Godzik A, Elsliger MA, Deacon AM, Wilson IA. Structure of an MmyB-like regulator from C. aurantiacus, member of a new transcription factor family linked to antibiotic metabolism in actinomycetes. PLoS One. 2012; 7(7):e41359. PMID: 22844465.
        View in: PubMed
      59. Xu Q, Göhler AK, Kosfeld A, Carlton D, Chiu HJ, Klock HE, Knuth MW, Miller MD, Elsliger MA, Deacon AM, Godzik A, Lesley SA, Jahreis K, Wilson IA. The structure of Mlc titration factor A (MtfA/YeeI) reveals a prototypical zinc metallopeptidase related to anthrax lethal factor. J Bacteriol. 2012 Jun; 194(11):2987-99. PMID: 22467785; PMCID: PMC3370624.
      60. Xu Q, Christen B, Chiu HJ, Jaroszewski L, Klock HE, Knuth MW, Miller MD, Elsliger MA, Deacon AM, Godzik A, Lesley SA, Figurski DH, Shapiro L, Wilson IA. Structure of the pilus assembly protein TadZ from Eubacterium rectale: implications for polar localization. Mol Microbiol. 2012 Feb; 83(4):712-27. PMID: 22211578.
        View in: PubMed
      61. Zhang Y, Zagnitko O, Rodionova I, Osterman A, Godzik A. The FGGY carbohydrate kinase family: insights into the evolution of functional specificities. PLoS Comput Biol. 2011 Dec; 7(12):e1002318. PMID: 22215998; PMCID: PMC3245297.
      62. D'Osualdo A, Weichenberger CX, Wagner RN, Godzik A, Wooley J, Reed JC. CARD8 and NLRP1 undergo autoproteolytic processing through a ZU5-like domain. PLoS One. 2011; 6(11):e27396. PMID: 22087307; PMCID: PMC3210808.
      63. Xu Q, Rawlings ND, Farr CL, Chiu HJ, Grant JC, Jaroszewski L, Klock HE, Knuth MW, Miller MD, Weekes D, Elsliger MA, Deacon AM, Godzik A, Lesley SA, Wilson IA. Structural and sequence analysis of imelysin-like proteins implicated in bacterial iron uptake. PLoS One. 2011; 6(7):e21875. PMID: 21799754.
        View in: PubMed
      64. Xu Q, Rawlings ND, Chiu HJ, Jaroszewski L, Klock HE, Knuth MW, Miller MD, Elsliger MA, Deacon AM, Godzik A, Lesley SA, Wilson IA. Structural analysis of papain-like NlpC/P60 superfamily enzymes with a circularly permuted topology reveals potential lipid binding sites. PLoS One. 2011; 6(7):e22013. PMID: 21799766.
        View in: PubMed
      65. Kazanov MD, Igarashi Y, Eroshkin AM, Cieplak P, Ratnikov B, Zhang Y, Li Z, Godzik A, Osterman AL, Smith JW. Structural determinants of limited proteolysis. J Proteome Res. 2011 Aug 05; 10(8):3642-51. PMID: 21682278; PMCID: PMC3164237.
      66. Jaroszewski L, Li Z, Cai XH, Weber C, Godzik A. FFAS server: novel features and applications. Nucleic Acids Res. 2011 Jul; 39(Web Server issue):W38-44. PMID: 21715387.
        View in: PubMed
      67. Cai XH, Jaroszewski L, Wooley J, Godzik A. Internal organization of large protein families: relationship between the sequence, structure, and function-based clustering. Proteins. 2011 Aug; 79(8):2389-402. PMID: 21671455.
        View in: PubMed
      68. Zakharov MN, Pillai BK, Bhasin S, Ulloor J, Istomin AY, Guo C, Godzik A, Kumar R, Jasuja R. Dynamics of coregulator-induced conformational perturbations in androgen receptor ligand binding domain. Mol Cell Endocrinol. 2011 Jul 20; 341(1-2):1-8. PMID: 21605623.
        View in: PubMed
      69. Han GW, Ko J, Farr CL, Deller MC, Xu Q, Chiu HJ, Miller MD, Sefcikova J, Somarowthu S, Beuning PJ, Elsliger MA, Deacon AM, Godzik A, Lesley SA, Wilson IA, Ondrechen MJ. Crystal structure of a metal-dependent phosphoesterase (YP_910028.1) from Bifidobacterium adolescentis: Computational prediction and experimental validation of phosphoesterase activity. Proteins. 2011 Jul; 79(7):2146-60. PMID: 21538547; PMCID: PMC3115465.
      70. Godzik A. Metagenomics and the protein universe. Curr Opin Struct Biol. 2011 Jun; 21(3):398-403. PMID: 21497084; PMCID: PMC3118404.
      71. Das D, Hervé M, Feuerhelm J, Farr CL, Chiu HJ, Elsliger MA, Knuth MW, Klock HE, Miller MD, Godzik A, Lesley SA, Deacon AM, Mengin-Lecreulx D, Wilson IA. Structure and function of the first full-length murein peptide ligase (Mpl) cell wall recycling protein. PLoS One. 2011 Mar 18; 6(3):e17624. PMID: 21445265; PMCID: PMC3060825.
      72. Zmasek CM, Godzik A. Strong functional patterns in the evolution of eukaryotic genomes revealed by the reconstruction of ancestral protein domain repertoires. Genome Biol. 2011; 12(1):R4. PMID: 21241503; PMCID: PMC3091302.
      73. Stranzl GR, Santelli E, Bankston LA, La Clair C, Bobkov A, Schwarzenbacher R, Godzik A, Perego M, Grynberg M, Liddington RC. Structural insights into inhibition of Bacillus anthracis sporulation by a novel class of non-heme globin sensor domains. J Biol Chem. 2011 Mar 11; 286(10):8448-58. PMID: 21216948; PMCID: PMC3048729.
      74. Zhang Q, Zmasek CM, Cai X, Godzik A. TIR domain-containing adaptor SARM is a late addition to the ongoing microbe-host dialog. Dev Comp Immunol. 2011 Apr; 35(4):461-8. PMID: 21110998; PMCID: PMC3085110.
      75. Das D, Finn RD, Abdubek P, Astakhova T, Axelrod HL, Bakolitsa C, Cai X, Carlton D, Chen C, Chiu HJ, Chiu M, Clayton T, Deller MC, Duan L, Ellrott K, Farr CL, Feuerhelm J, Grant JC, Grzechnik A, Han GW, Jaroszewski L, Jin KK, Klock HE, Knuth MW, Kozbial P, Krishna SS, Kumar A, Lam WW, Marciano D, Miller MD, Morse AT, Nigoghossian E, Nopakun A, Okach L, Puckett C, Reyes R, Tien HJ, Trame CB, van den Bedem H, Weekes D, Wooten T, Xu Q, Yeh A, Zhou J, Hodgson KO, Wooley J, Elsliger MA, Deacon AM, Godzik A, Lesley SA, Wilson IA. The crystal structure of a bacterial Sufu-like protein defines a novel group of bacterial proteins that are similar to the N-terminal domain of human Sufu. Protein Sci. 2010 Nov; 19(11):2131-40. PMID: 20836087.
        View in: PubMed
      76. Pawlowski K, Muszewska A, Lenart A, Szczepinska T, Godzik A, Grynberg M. A widespread peroxiredoxin-like domain present in tumor suppression- and progression-implicated proteins. BMC Genomics. 2010 Oct 21; 11:590. PMID: 20964819; PMCID: PMC3091736.
      77. Ellrott K, Zmasek CM, Weekes D, Sri Krishna S, Bakolitsa C, Godzik A, Wooley J. TOPSAN: a dynamic web database for structural genomics. Nucleic Acids Res. 2011 Jan; 39(Database issue):D494-6. PMID: 20961957; PMCID: PMC3013775.
      78. Prlic A, Bliven S, Rose PW, Bluhm WF, Bizon C, Godzik A, Bourne PE. Pre-calculated protein structure alignments at the RCSB PDB website. Bioinformatics. 2010 Dec 1; 26(23):2983-5. PMID: 20937596.
        View in: PubMed
      79. Xu Q, Eguchi T, Mathews II, Rife CL, Chiu HJ, Farr CL, Feuerhelm J, Jaroszewski L, Klock HE, Knuth MW, Miller MD, Weekes D, Elsliger MA, Deacon AM, Godzik A, Lesley SA, Wilson IA. Insights into substrate specificity of geranylgeranyl reductases revealed by the structure of digeranylgeranylglycerophospholipid reductase, an essential enzyme in the biosynthesis of archaeal membrane lipids. J Mol Biol. 2010 Dec 3; 404(3):403-17. PMID: 20869368.
        View in: PubMed
      80. Elsliger MA, Deacon AM, Godzik A, Lesley SA, Wooley J, Wüthrich K, Wilson IA. The JCSG high-throughput structural biology pipeline. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010 Oct 01; 66(Pt 10):1137-42. PMID: 20944202; PMCID: PMC2954196.
      81. Krishna SS, Weekes D, Bakolitsa C, Elsliger MA, Wilson IA, Godzik A, Wooley J. TOPSAN: use of a collaborative environment for annotating, analyzing and disseminating data on JCSG and PSI structures. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010 Oct 01; 66(Pt 10):1143-7. PMID: 20944203; PMCID: PMC2954197.
      82. Han GW, Yang XL, McMullan D, Chong YE, Krishna SS, Rife CL, Weekes D, Brittain SM, Abdubek P, Ambing E, Astakhova T, Axelrod HL, Carlton D, Caruthers J, Chiu HJ, Clayton T, Duan L, Feuerhelm J, Grant JC, Grzechnik SK, Jaroszewski L, Jin KK, Klock HE, Knuth MW, Kumar A, Marciano D, Miller MD, Morse AT, Nigoghossian E, Okach L, Paulsen J, Reyes R, van den Bedem H, White A, Wolf G, Xu Q, Hodgson KO, Wooley J, Deacon AM, Godzik A, Lesley SA, Elsliger MA, Schimmel P, Wilson IA. Structure of a tryptophanyl-tRNA synthetase containing an iron-sulfur cluster. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010 Oct 1; 66(Pt 10):1326-34. PMID: 20944229.
        View in: PubMed
      83. Bakolitsa C, Xu Q, Rife CL, Abdubek P, Astakhova T, Axelrod HL, Carlton D, Chen C, Chiu HJ, Clayton T, Das D, Deller MC, Duan L, Ellrott K, Farr CL, Feuerhelm J, Grant JC, Grzechnik A, Han GW, Jaroszewski L, Jin KK, Klock HE, Knuth MW, Kozbial P, Krishna SS, Kumar A, Lam WW, Marciano D, McMullan D, Miller MD, Morse AT, Nigoghossian E, Nopakun A, Okach L, Puckett C, Reyes R, Tien HJ, Trame CB, van den Bedem H, Weekes D, Hodgson KO, Wooley J, Elsliger MA, Deacon AM, Godzik A, Lesley SA, Wilson IA. Structure of BT_3984, a member of the SusD/RagB family of nutrient-binding molecules. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010 Oct 1; 66(Pt 10):1274-80. PMID: 20944222.
        View in: PubMed
      84. Weekes D, Krishna SS, Bakolitsa C, Wilson IA, Godzik A, Wooley J. TOPSAN: a collaborative annotation environment for structural genomics. BMC Bioinformatics. 2010 Aug 17; 11:426. PMID: 20716366; PMCID: PMC2936398.
      85. Yeh AP, Abdubek P, Astakhova T, Axelrod HL, Bakolitsa C, Cai X, Carlton D, Chen C, Chiu HJ, Chiu M, Clayton T, Das D, Deller MC, Duan L, Ellrott K, Farr CL, Feuerhelm J, Grant JC, Grzechnik A, Han GW, Jaroszewski L, Jin KK, Klock HE, Knuth MW, Kozbial P, Krishna SS, Kumar A, Lam WW, Marciano D, McMullan D, Miller MD, Morse AT, Nigoghossian E, Nopakun A, Okach L, Puckett C, Reyes R, Tien HJ, Trame CB, van den Bedem H, Weekes D, Wooten T, Xu Q, Hodgson KO, Wooley J, Elsliger MA, Deacon AM, Godzik A, Lesley SA, Wilson IA. Structure of Bacteroides thetaiotaomicron BT2081 at 2.05 Å resolution: the first structural representative of a new protein family that may play a role in carbohydrate metabolism. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010 Oct 1; 66(Pt 10):1287-96. PMID: 20944224.
        View in: PubMed
      86. Axelrod HL, Das D, Abdubek P, Astakhova T, Bakolitsa C, Carlton D, Chen C, Chiu HJ, Clayton T, Deller MC, Duan L, Ellrott K, Farr CL, Feuerhelm J, Grant JC, Grzechnik A, Han GW, Jaroszewski L, Jin KK, Klock HE, Knuth MW, Kozbial P, Krishna SS, Kumar A, Lam WW, Marciano D, McMullan D, Miller MD, Morse AT, Nigoghossian E, Nopakun A, Okach L, Puckett C, Reyes R, Sefcovic N, Tien HJ, Trame CB, van den Bedem H, Weekes D, Wooten T, Xu Q, Hodgson KO, Wooley J, Elsliger MA, Deacon AM, Godzik A, Lesley SA, Wilson IA. Structures of three members of Pfam PF02663 (FmdE) implicated in microbial methanogenesis reveal a conserved a+ß core domain and an auxiliary C-terminal treble-clef zinc finger. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010 Oct 1; 66(Pt 10):1335-46. PMID: 20944230.
        View in: PubMed
      87. Han GW, Elsliger MA, Yeates TO, Xu Q, Murzin AG, Krishna SS, Jaroszewski L, Abdubek P, Astakhova T, Axelrod HL, Carlton D, Chen C, Chiu HJ, Clayton T, Das D, Deller MC, Duan L, Ernst D, Feuerhelm J, Grant JC, Grzechnik A, Jin KK, Johnson HA, Klock HE, Knuth MW, Kozbial P, Kumar A, Lam WW, Marciano D, McMullan D, Miller MD, Morse AT, Nigoghossian E, Okach L, Reyes R, Rife CL, Sefcovic N, Tien HJ, Trame CB, van den Bedem H, Weekes D, Hodgson KO, Wooley J, Deacon AM, Godzik A, Lesley SA, Wilson IA. Structure of a putative NTP pyrophosphohydrolase: YP_001813558.1 from Exiguobacterium sibiricum 255-15. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010 Oct 1; 66(Pt 10):1237-44. PMID: 20944217.
        View in: PubMed
      88. Xu Q, Abdubek P, Astakhova T, Axelrod HL, Bakolitsa C, Cai X, Carlton D, Chen C, Chiu HJ, Clayton T, Das D, Deller MC, Duan L, Ellrott K, Farr CL, Feuerhelm J, Grant JC, Grzechnik A, Han GW, Jaroszewski L, Jin KK, Klock HE, Knuth MW, Kozbial P, Krishna SS, Kumar A, Lam WW, Marciano D, Miller MD, Morse AT, Nigoghossian E, Nopakun A, Okach L, Puckett C, Reyes R, Tien HJ, Trame CB, van den Bedem H, Weekes D, Wooten T, Yeh A, Zhou J, Hodgson KO, Wooley J, Elsliger MA, Deacon AM, Godzik A, Lesley SA, Wilson IA. Structure of a membrane-attack complex/perforin (MACPF) family protein from the human gut symbiont Bacteroides thetaiotaomicron. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010 Oct 1; 66(Pt 10):1297-305. PMID: 20944225.
        View in: PubMed
      89. Chiu HJ, Abdubek P, Astakhova T, Axelrod HL, Carlton D, Clayton T, Das D, Deller MC, Duan L, Feuerhelm J, Grant JC, Grzechnik A, Han GW, Jaroszewski L, Jin KK, Klock HE, Knuth MW, Kozbial P, Krishna SS, Kumar A, Marciano D, McMullan D, Miller MD, Morse AT, Nigoghossian E, Okach L, Reyes R, Tien HJ, Trame CB, van den Bedem H, Weekes D, Xu Q, Hodgson KO, Wooley J, Elsliger MA, Deacon AM, Godzik A, Lesley SA, Wilson IA. The structure of Haemophilus influenzae prephenate dehydrogenase suggests unique features of bifunctional TyrA enzymes. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010 Oct 1; 66(Pt 10):1317-25. PMID: 20944228.
        View in: PubMed
      90. Xu Q, Abdubek P, Astakhova T, Axelrod HL, Bakolitsa C, Cai X, Carlton D, Chen C, Chiu HJ, Chiu M, Clayton T, Das D, Deller MC, Duan L, Ellrott K, Farr CL, Feuerhelm J, Grant JC, Grzechnik A, Han GW, Jaroszewski L, Jin KK, Klock HE, Knuth MW, Kozbial P, Krishna SS, Kumar A, Lam WW, Marciano D, Miller MD, Morse AT, Nigoghossian E, Nopakun A, Okach L, Puckett C, Reyes R, Tien HJ, Trame CB, van den Bedem H, Weekes D, Wooten T, Yeh A, Hodgson KO, Wooley J, Elsliger MA, Deacon AM, Godzik A, Lesley SA, Wilson IA. Structure of the ?-D-glutamyl-L-diamino acid endopeptidase YkfC from Bacillus cereus in complex with L-Ala-?-D-Glu: insights into substrate recognition by NlpC/P60 cysteine peptidases. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010 Oct 1; 66(Pt 10):1354-64. PMID: 20944232.
        View in: PubMed
      91. Xu Q, Abdubek P, Astakhova T, Axelrod HL, Bakolitsa C, Cai X, Carlton D, Chen C, Chiu HJ, Chiu M, Clayton T, Das D, Deller MC, Duan L, Ellrott K, Farr CL, Feuerhelm J, Grant JC, Grzechnik A, Han GW, Jaroszewski L, Jin KK, Klock HE, Knuth MW, Kozbial P, Krishna SS, Kumar A, Marciano D, McMullan D, Miller MD, Morse AT, Nigoghossian E, Nopakun A, Okach L, Puckett C, Reyes R, Sefcovic N, Tien HJ, Trame CB, van den Bedem H, Weekes D, Wooten T, Yeh A, Zhou J, Hodgson KO, Wooley J, Elsliger MA, Deacon AM, Godzik A, Lesley SA, Wilson IA. A conserved fold for fimbrial components revealed by the crystal structure of a putative fimbrial assembly protein (BT1062) from Bacteroides thetaiotaomicron at 2.2 Å resolution. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010 Oct 1; 66(Pt 10):1281-6. PMID: 20944223.
        View in: PubMed
      92. Miller MD, Aravind L, Bakolitsa C, Rife CL, Carlton D, Abdubek P, Astakhova T, Axelrod HL, Chiu HJ, Clayton T, Deller MC, Duan L, Feuerhelm J, Grant JC, Han GW, Jaroszewski L, Jin KK, Klock HE, Knuth MW, Kozbial P, Krishna SS, Kumar A, Marciano D, McMullan D, Morse AT, Nigoghossian E, Okach L, Reyes R, van den Bedem H, Weekes D, Xu Q, Hodgson KO, Wooley J, Elsliger MA, Deacon AM, Godzik A, Lesley SA, Wilson IA. Structure of the first representative of Pfam family PF04016 (DUF364) reveals enolase and Rossmann-like folds that combine to form a unique active site with a possible role in heavy-metal chelation. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010 Oct 1; 66(Pt 10):1167-73. PMID: 20944207.
        View in: PubMed
      93. Ellrott K, Jaroszewski L, Li W, Wooley JC, Godzik A. Expansion of the protein repertoire in newly explored environments: human gut microbiome specific protein families. PLoS Comput Biol. 2010 Jun; 6(6):e1000798. PMID: 20532204.
        View in: PubMed
      94. Nakamura T, Cieplak P, Cho DH, Godzik A, Lipton SA. S-nitrosylation of Drp1 links excessive mitochondrial fission to neuronal injury in neurodegeneration. Mitochondrion. 2010 Aug; 10(5):573-8. PMID: 20447471.
        View in: PubMed
      95. Matsumoto Y, Xu Q, Miyazaki S, Kaito C, Farr CL, Axelrod HL, Chiu HJ, Klock HE, Knuth MW, Miller MD, Elsliger MA, Deacon AM, Godzik A, Lesley SA, Sekimizu K, Wilson IA. Structure of a virulence regulatory factor CvfB reveals a novel winged helix RNA binding module. Structure. 2010 Mar 14; 18(4):537-47. PMID: 20399190; PMCID: PMC2858061.
      96. Das D, Finn RD, Carlton D, Miller MD, Abdubek P, Astakhova T, Axelrod HL, Bakolitsa C, Chen C, Chiu HJ, Chiu M, Clayton T, Deller MC, Duan L, Ellrott K, Ernst D, Farr CL, Feuerhelm J, Grant JC, Grzechnik A, Han GW, Jaroszewski L, Jin KK, Klock HE, Knuth MW, Kozbial P, Krishna SS, Kumar A, Marciano D, McMullan D, Morse AT, Nigoghossian E, Nopakun A, Okach L, Puckett C, Reyes R, Rife CL, Sefcovic N, Tien HJ, Trame CB, van den Bedem H, Weekes D, Wooten T, Xu Q, Hodgson KO, Wooley J, Elsliger MA, Deacon AM, Godzik A, Lesley SA, Wilson IA. The structure of BVU2987 from Bacteroides vulgatus reveals a superfamily of bacterial periplasmic proteins with possible inhibitory function. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010 Oct 1; 66(Pt 10):1265-73. PMID: 20944221.
        View in: PubMed
      97. Bakolitsa C, Kumar A, Jin KK, McMullan D, Krishna SS, Miller MD, Abdubek P, Acosta C, Astakhova T, Axelrod HL, Burra P, Carlton D, Chen C, Chiu HJ, Clayton T, Das D, Deller MC, Duan L, Elias Y, Ellrott K, Ernst D, Farr CL, Feuerhelm J, Grant JC, Grzechnik A, Grzechnik SK, Han GW, Jaroszewski L, Johnson HA, Klock HE, Knuth MW, Kozbial P, Marciano D, Morse AT, Murphy KD, Nigoghossian E, Nopakun A, Okach L, Paulsen J, Puckett C, Reyes R, Rife CL, Sefcovic N, Tien HJ, Trame CB, Trout CV, van den Bedem H, Weekes D, White A, Xu Q, Hodgson KO, Wooley J, Elsliger MA, Deacon AM, Godzik A, Lesley SA, Wilson IA. Structures of the first representatives of Pfam family PF06684 (DUF1185) reveal a novel variant of the Bacillus chorismate mutase fold and suggest a role in amino-acid metabolism. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010 Oct 1; 66(Pt 10):1182-9. PMID: 20944209.
        View in: PubMed
      98. Han GW, Bakolitsa C, Miller MD, Kumar A, Carlton D, Najmanovich RJ, Abdubek P, Astakhova T, Axelrod HL, Chen C, Chiu HJ, Clayton T, Das D, Deller MC, Duan L, Ernst D, Feuerhelm J, Grant JC, Grzechnik A, Jaroszewski L, Jin KK, Johnson HA, Klock HE, Knuth MW, Kozbial P, Krishna SS, Marciano D, McMullan D, Morse AT, Nigoghossian E, Okach L, Reyes R, Rife CL, Sefcovic N, Tien HJ, Trame CB, van den Bedem H, Weekes D, Xu Q, Hodgson KO, Wooley J, Elsliger MA, Deacon AM, Godzik A, Lesley SA, Wilson IA. Structures of the first representatives of Pfam family PF06938 (DUF1285) reveal a new fold with repeated structural motifs and possible involvement in signal transduction. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010 Oct 1; 66(Pt 10):1218-25. PMID: 20944214.
        View in: PubMed
      99. Krishna SS, Aravind L, Bakolitsa C, Caruthers J, Carlton D, Miller MD, Abdubek P, Astakhova T, Axelrod HL, Chiu HJ, Clayton T, Deller MC, Duan L, Feuerhelm J, Grant JC, Han GW, Jaroszewski L, Jin KK, Klock HE, Knuth MW, Kumar A, Marciano D, McMullan D, Morse AT, Nigoghossian E, Okach L, Reyes R, Rife CL, van den Bedem H, Weekes D, Xu Q, Hodgson KO, Wooley J, Elsliger MA, Deacon AM, Godzik A, Lesley SA, Wilson IA. The structure of SSO2064, the first representative of Pfam family PF01796, reveals a novel two-domain zinc-ribbon OB-fold architecture with a potential acyl-CoA-binding role. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010 Oct 1; 66(Pt 10):1160-6. PMID: 20944206.
        View in: PubMed
      100. Zhang Q, Zmasek CM, Godzik A. Domain architecture evolution of pattern-recognition receptors. Immunogenetics. 2010 May; 62(5):263-72. PMID: 20195594; PMCID: PMC2858798.
      101. Wooley JC, Godzik A, Friedberg I. A primer on metagenomics. PLoS Comput Biol. 2010 Feb 26; 6(2):e1000667. PMID: 20195499; PMCID: PMC2829047.
      102. Das D, Moiani D, Axelrod HL, Miller MD, McMullan D, Jin KK, Abdubek P, Astakhova T, Burra P, Carlton D, Chiu HJ, Clayton T, Deller MC, Duan L, Ernst D, Feuerhelm J, Grant JC, Grzechnik A, Grzechnik SK, Han GW, Jaroszewski L, Klock HE, Knuth MW, Kozbial P, Krishna SS, Kumar A, Marciano D, Morse AT, Nigoghossian E, Okach L, Paulsen J, Reyes R, Rife CL, Sefcovic N, Tien HJ, Trame CB, van den Bedem H, Weekes D, Xu Q, Hodgson KO, Wooley J, Elsliger MA, Deacon AM, Godzik A, Lesley SA, Tainer JA, Wilson IA. Crystal structure of the first eubacterial Mre11 nuclease reveals novel features that may discriminate substrates during DNA repair. J Mol Biol. 2010 Apr 2; 397(3):647-63. PMID: 20122942.
        View in: PubMed
      103. Chiu HJ, Bakolitsa C, Skerra A, Lomize A, Carlton D, Miller MD, Krishna SS, Abdubek P, Astakhova T, Axelrod HL, Clayton T, Deller MC, Duan L, Feuerhelm J, Grant JC, Grzechnik SK, Han GW, Jaroszewski L, Jin KK, Klock HE, Knuth MW, Kozbial P, Kumar A, Marciano D, McMullan D, Morse AT, Nigoghossian E, Okach L, Paulsen J, Reyes R, Rife CL, van den Bedem H, Weekes D, Xu Q, Hodgson KO, Wooley J, Elsliger MA, Deacon AM, Godzik A, Lesley SA, Wilson IA. Structure of the first representative of Pfam family PF09410 (DUF2006) reveals a structural signature of the calycin superfamily that suggests a role in lipid metabolism. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010 Oct 1; 66(Pt 10):1153-9. PMID: 20944205.
        View in: PubMed
      104. Kumar A, Lomize A, Jin KK, Carlton D, Miller MD, Jaroszewski L, Abdubek P, Astakhova T, Axelrod HL, Chiu HJ, Clayton T, Das D, Deller MC, Duan L, Feuerhelm J, Grant JC, Grzechnik A, Han GW, Klock HE, Knuth MW, Kozbial P, Krishna SS, Marciano D, McMullan D, Morse AT, Nigoghossian E, Okach L, Reyes R, Rife CL, Sefcovic N, Tien HJ, Trame CB, van den Bedem H, Weekes D, Xu Q, Hodgson KO, Wooley J, Elsliger MA, Deacon AM, Godzik A, Lesley SA, Wilson IA. Open and closed conformations of two SpoIIAA-like proteins (YP_749275.1 and YP_001095227.1) provide insights into membrane association and ligand binding. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010 Oct 1; 66(Pt 10):1245-53. PMID: 20944218.
        View in: PubMed
      105. Xu Q, Bateman A, Finn RD, Abdubek P, Astakhova T, Axelrod HL, Bakolitsa C, Carlton D, Chen C, Chiu HJ, Chiu M, Clayton T, Das D, Deller MC, Duan L, Ellrott K, Ernst D, Farr CL, Feuerhelm J, Grant JC, Grzechnik A, Han GW, Jaroszewski L, Jin KK, Klock HE, Knuth MW, Kozbial P, Krishna SS, Kumar A, Marciano D, McMullan D, Miller MD, Morse AT, Nigoghossian E, Nopakun A, Okach L, Puckett C, Reyes R, Rife CL, Sefcovic N, Tien HJ, Trame CB, van den Bedem H, Weekes D, Wooten T, Hodgson KO, Wooley J, Elsliger MA, Deacon AM, Godzik A, Lesley SA, Wilson IA. Bacterial pleckstrin homology domains: a prokaryotic origin for the PH domain. J Mol Biol. 2010 Feb 12; 396(1):31-46. PMID: 19913036.
        View in: PubMed
      106. Bakolitsa C, Bateman A, Jin KK, McMullan D, Krishna SS, Miller MD, Abdubek P, Acosta C, Astakhova T, Axelrod HL, Burra P, Carlton D, Chiu HJ, Clayton T, Das D, Deller MC, Duan L, Elias Y, Feuerhelm J, Grant JC, Grzechnik A, Grzechnik SK, Han GW, Jaroszewski L, Klock HE, Knuth MW, Kozbial P, Kumar A, Marciano D, Morse AT, Murphy KD, Nigoghossian E, Okach L, Oommachen S, Paulsen J, Reyes R, Rife CL, Sefcovic N, Tien H, Trame CB, Trout CV, van den Bedem H, Weekes D, White A, Xu Q, Hodgson KO, Wooley J, Elsliger MA, Deacon AM, Godzik A, Lesley S, Wilson IA. The structure of Jann_2411 (DUF1470) from Jannaschia sp. at 1.45 Å resolution reveals a new fold (the ABATE domain) and suggests its possible role as a transcription regulator. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010 Oct 1; 66(Pt 10):1198-204. PMID: 20944211.
        View in: PubMed
      107. Das D, Kozbial P, Han GW, Carlton D, Jaroszewski L, Abdubek P, Astakhova T, Axelrod HL, Bakolitsa C, Chen C, Chiu HJ, Chiu M, Clayton T, Deller MC, Duan L, Ellrott K, Elsliger MA, Ernst D, Farr CL, Feuerhelm J, Grzechnik A, Grant JC, Jin KK, Johnson HA, Klock HE, Knuth MW, Krishna SS, Kumar A, Marciano D, McMullan D, Miller MD, Morse AT, Nigoghossian E, Nopakun A, Okach L, Oommachen S, Paulsen J, Puckett C, Reyes R, Rife CL, Sefcovic N, Tien HJ, Trame CB, van den Bedem H, Weekes D, Wooten T, Xu Q, Hodgson KO, Wooley J, Deacon AM, Godzik A, Lesley SA, Wilson IA. The structure of KPN03535 (gi|152972051), a novel putative lipoprotein from Klebsiella pneumoniae, reveals an OB-fold. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010 Oct 1; 66(Pt 10):1254-60. PMID: 20944219.
        View in: PubMed
      108. Xu Q, McMullan D, Jaroszewski L, Krishna SS, Elsliger MA, Yeh AP, Abdubek P, Astakhova T, Axelrod HL, Carlton D, Chiu HJ, Clayton T, Duan L, Feuerhelm J, Grant J, Han GW, Jin KK, Klock HE, Knuth MW, Miller MD, Morse AT, Nigoghossian E, Okach L, Oommachen S, Paulsen J, Reyes R, Rife CL, van den Bedem H, Hodgson KO, Wooley J, Deacon AM, Godzik A, Lesley SA, Wilson IA. Structure of an essential bacterial protein YeaZ (TM0874) from Thermotoga maritima at 2.5 Å resolution. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010 Oct 1; 66(Pt 10):1230-6. PMID: 20944216.
        View in: PubMed
      109. Bakolitsa C, Kumar A, Carlton D, Miller MD, Krishna SS, Abdubek P, Astakhova T, Axelrod HL, Chiu HJ, Clayton T, Deller MC, Duan L, Elsliger MA, Feuerhelm J, Grzechnik SK, Grant JC, Han GW, Jaroszewski L, Jin KK, Klock HE, Knuth MW, Kozbial P, Marciano D, McMullan D, Morse AT, Nigoghossian E, Okach L, Oommachen S, Paulsen J, Reyes R, Rife CL, Tien HJ, Trout CV, van den Bedem H, Weekes D, Xu Q, Hodgson KO, Wooley J, Deacon AM, Godzik A, Lesley SA, Wilson IA. Structure of LP2179, the first representative of Pfam family PF08866, suggests a new fold with a role in amino-acid metabolism. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010 Oct 1; 66(Pt 10):1205-10. PMID: 20944212.
        View in: PubMed
      110. Bakolitsa C, Kumar A, McMullan D, Krishna SS, Miller MD, Carlton D, Najmanovich R, Abdubek P, Astakhova T, Chiu HJ, Clayton T, Deller MC, Duan L, Elias Y, Feuerhelm J, Grant JC, Grzechnik SK, Han GW, Jaroszewski L, Jin KK, Klock HE, Knuth MW, Kozbial P, Marciano D, Morse AT, Nigoghossian E, Okach L, Oommachen S, Paulsen J, Reyes R, Rife CL, Trout CV, van den Bedem H, Weekes D, White A, Xu Q, Hodgson KO, Wooley J, Elsliger MA, Deacon AM, Godzik A, Lesley SA, Wilson IA. The structure of the first representative of Pfam family PF06475 reveals a new fold with possible involvement in glycolipid metabolism. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010 Oct 1; 66(Pt 10):1211-7. PMID: 20944213.
        View in: PubMed
      111. Das D, Grishin NV, Kumar A, Carlton D, Bakolitsa C, Miller MD, Abdubek P, Astakhova T, Axelrod HL, Burra P, Chen C, Chiu HJ, Chiu M, Clayton T, Deller MC, Duan L, Ellrott K, Ernst D, Farr CL, Feuerhelm J, Grzechnik A, Grzechnik SK, Grant JC, Han GW, Jaroszewski L, Jin KK, Johnson HA, Klock HE, Knuth MW, Kozbial P, Krishna SS, Marciano D, McMullan D, Morse AT, Nigoghossian E, Nopakun A, Okach L, Oommachen S, Paulsen J, Puckett C, Reyes R, Rife CL, Sefcovic N, Tien HJ, Trame CB, van den Bedem H, Weekes D, Wooten T, Xu Q, Hodgson KO, Wooley J, Elsliger MA, Deacon AM, Godzik A, Lesley SA, Wilson IA. The structure of the first representative of Pfam family PF09836 reveals a two-domain organization and suggests involvement in transcriptional regulation. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010 Oct 1; 66(Pt 10):1174-81. PMID: 20944208.
        View in: PubMed
      112. Axelrod HL, Kozbial P, McMullan D, Krishna SS, Miller MD, Abdubek P, Acosta C, Astakhova T, Carlton D, Caruthers J, Chiu HJ, Clayton T, Deller MC, Duan L, Elias Y, Feuerhelm J, Grzechnik SK, Grant JC, Han GW, Jaroszewski L, Jin KK, Klock HE, Knuth MW, Kumar A, Marciano D, Morse AT, Murphy KD, Nigoghossian E, Okach L, Oommachen S, Paulsen J, Reyes R, Rife CL, Tien HJ, Trout CV, van den Bedem H, Weekes D, White A, Xu Q, Zubieta C, Hodgson KO, Wooley J, Elsliger MA, Deacon AM, Godzik A, Lesley SA, Wilson IA. Conformational changes associated with the binding of zinc acetate at the putative active site of XcTcmJ, a cupin from Xanthomonas campestris pv. campestris. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010 Oct 1; 66(Pt 10):1347-53. PMID: 20944231.
        View in: PubMed
      113. Jaroszewski L, Li Z, Krishna SS, Bakolitsa C, Wooley J, Deacon AM, Wilson IA, Godzik A. Exploration of uncharted regions of the protein universe. PLoS Biol. 2009 Sep; 7(9):e1000205. PMID: 19787035.
        View in: PubMed
      114. Zhang Y, Thiele I, Weekes D, Li Z, Jaroszewski L, Ginalski K, Deacon AM, Wooley J, Lesley SA, Wilson IA, Palsson B, Osterman A, Godzik A. Three-dimensional structural view of the central metabolic network of Thermotoga maritima. Science. 2009 Sep 18; 325(5947):1544-9. PMID: 19762644.
        View in: PubMed
      115. Istomin AY, Godzik A. Understanding diversity of human innate immunity receptors: analysis of surface features of leucine-rich repeat domains in NLRs and TLRs. BMC Immunol. 2009 Sep 03; 10:48. PMID: 19728889; PMCID: PMC2747839.
      116. Xu Q, Traag BA, Willemse J, McMullan D, Miller MD, Elsliger MA, Abdubek P, Astakhova T, Axelrod HL, Bakolitsa C, Carlton D, Chen C, Chiu HJ, Chruszcz M, Clayton T, Das D, Deller MC, Duan L, Ellrott K, Ernst D, Farr CL, Feuerhelm J, Grant JC, Grzechnik A, Grzechnik SK, Han GW, Jaroszewski L, Jin KK, Klock HE, Knuth MW, Kozbial P, Krishna SS, Kumar A, Marciano D, Minor W, Mommaas AM, Morse AT, Nigoghossian E, Nopakun A, Okach L, Oommachen S, Paulsen J, Puckett C, Reyes R, Rife CL, Sefcovic N, Tien HJ, Trame CB, van den Bedem H, Wang S, Weekes D, Hodgson KO, Wooley J, Deacon AM, Godzik A, Lesley SA, Wilson IA, van Wezel GP. Structural and functional characterizations of SsgB, a conserved activator of developmental cell division in morphologically complex actinomycetes. J Biol Chem. 2009 Sep 11; 284(37):25268-79. PMID: 19567872.
        View in: PubMed
      117. Burra PV, Zhang Y, Godzik A, Stec B. Global distribution of conformational states derived from redundant models in the PDB points to non-uniqueness of the protein structure. Proc Natl Acad Sci U S A. 2009 Jun 30; 106(26):10505-10. PMID: 19553204; PMCID: PMC2705611.
      118. Dessailly BH, Nair R, Jaroszewski L, Fajardo JE, Kouranov A, Lee D, Fiser A, Godzik A, Rost B, Orengo C. PSI-2: structural genomics to cover protein domain family space. Structure. 2009 Jun 10; 17(6):869-81. PMID: 19523904.
        View in: PubMed
      119. Xu Q, Carlton D, Miller MD, Elsliger MA, Krishna SS, Abdubek P, Astakhova T, Burra P, Chiu HJ, Clayton T, Deller MC, Duan L, Elias Y, Feuerhelm J, Grant JC, Grzechnik A, Grzechnik SK, Han GW, Jaroszewski L, Jin KK, Klock HE, Knuth MW, Kozbial P, Kumar A, Marciano D, McMullan D, Morse AT, Nigoghossian E, Okach L, Oommachen S, Paulsen J, Reyes R, Rife CL, Sefcovic N, Trame C, Trout CV, van den Bedem H, Weekes D, Hodgson KO, Wooley J, Deacon AM, Godzik A, Lesley SA, Wilson IA. Crystal structure of histidine phosphotransfer protein ShpA, an essential regulator of stalk biogenesis in Caulobacter crescentus. J Mol Biol. 2009 Jul 24; 390(4):686-98. PMID: 19450606.
        View in: PubMed
      120. An Y, Chen CY, Moyer B, Rotkiewicz P, Elsliger MA, Godzik A, Wilson IA, Balch WE. Structural and functional analysis of the globular head domain of p115 provides insight into membrane tethering. J Mol Biol. 2009 Aug 07; 391(1):26-41. PMID: 19414022; PMCID: PMC2754402.
      121. Das D, Kozbial P, Axelrod HL, Miller MD, McMullan D, Krishna SS, Abdubek P, Acosta C, Astakhova T, Burra P, Carlton D, Chen C, Chiu HJ, Clayton T, Deller MC, Duan L, Elias Y, Elsliger MA, Ernst D, Farr C, Feuerhelm J, Grzechnik A, Grzechnik SK, Hale J, Han GW, Jaroszewski L, Jin KK, Johnson HA, Klock HE, Knuth MW, Kumar A, Marciano D, Morse AT, Murphy KD, Nigoghossian E, Nopakun A, Okach L, Oommachen S, Paulsen J, Puckett C, Reyes R, Rife CL, Sefcovic N, Sudek S, Tien H, Trame C, Trout CV, van den Bedem H, Weekes D, White A, Xu Q, Hodgson KO, Wooley J, Deacon AM, Godzik A, Lesley SA, Wilson IA. Crystal structure of a novel Sm-like protein of putative cyanophage origin at 2.60 A resolution. Proteins. 2009 May 1; 75(2):296-307. PMID: 19173316.
        View in: PubMed
      122. Grynberg M, Godzik A. The signal for signaling, found. PLoS Pathog. 2009 Apr; 5(4):e1000398. PMID: 19390616; PMCID: PMC2668190.
      123. Cho DH, Nakamura T, Fang J, Cieplak P, Godzik A, Gu Z, Lipton SA. S-nitrosylation of Drp1 mediates beta-amyloid-related mitochondrial fission and neuronal injury. Science. 2009 Apr 3; 324(5923):102-5. PMID: 19342591.
        View in: PubMed
      124. Das D, Krishna SS, McMullan D, Miller MD, Xu Q, Abdubek P, Acosta C, Astakhova T, Axelrod HL, Burra P, Carlton D, Chiu HJ, Clayton T, Deller MC, Duan L, Elias Y, Elsliger MA, Ernst D, Feuerhelm J, Grzechnik A, Grzechnik SK, Hale J, Han GW, Jaroszewski L, Jin KK, Klock HE, Knuth MW, Kozbial P, Kumar A, Marciano D, Morse AT, Murphy KD, Nigoghossian E, Okach L, Oommachen S, Paulsen J, Reyes R, Rife CL, Sefcovic N, Tien H, Trame CB, Trout CV, van den Bedem H, Weekes D, White A, Hodgson KO, Wooley J, Deacon AM, Godzik A, Lesley SA, Wilson IA. Crystal structure of the Fic (Filamentation induced by cAMP) family protein SO4266 (gi|24375750) from Shewanella oneidensis MR-1 at 1.6 A resolution. Proteins. 2009 Apr; 75(1):264-71. PMID: 19127588.
        View in: PubMed
      125. Xu Q, Rife CL, Carlton D, Miller MD, Krishna SS, Elsliger MA, Abdubek P, Astakhova T, Chiu HJ, Clayton T, Duan L, Feuerhelm J, Grzechnik SK, Hale J, Han GW, Jaroszewski L, Jin KK, Klock HE, Knuth MW, Kumar A, McMullan D, Morse AT, Nigoghossian E, Okach L, Oommachen S, Paulsen J, Reyes R, van den Bedem H, Hodgson KO, Wooley J, Deacon AM, Godzik A, Lesley SA, Wilson IA. Crystal structure of a novel archaeal AAA+ ATPase SSO1545 from Sulfolobus solfataricus. Proteins. 2009 Mar; 74(4):1041-9. PMID: 19089981.
        View in: PubMed
      126. Schwede T, Sali A, Honig B, Levitt M, Berman HM, Jones D, Brenner SE, Burley SK, Das R, Dokholyan NV, Dunbrack RL, Fidelis K, Fiser A, Godzik A, Huang YJ, Humblet C, Jacobson MP, Joachimiak A, Krystek SR, Kortemme T, Kryshtafovych A, Montelione GT, Moult J, Murray D, Sanchez R, Sosnick TR, Standley DM, Stouch T, Vajda S, Vasquez M, Westbrook JD, Wilson IA. Outcome of a workshop on applications of protein models in biomedical research. Structure. 2009 Feb 13; 17(2):151-9. PMID: 19217386.
        View in: PubMed
      127. Xu Q, Sudek S, McMullan D, Miller MD, Geierstanger B, Jones DH, Krishna SS, Spraggon G, Bursalay B, Abdubek P, Acosta C, Ambing E, Astakhova T, Axelrod HL, Carlton D, Caruthers J, Chiu HJ, Clayton T, Deller MC, Duan L, Elias Y, Elsliger MA, Feuerhelm J, Grzechnik SK, Hale J, Han GW, Haugen J, Jaroszewski L, Jin KK, Klock HE, Knuth MW, Kozbial P, Kumar A, Marciano D, Morse AT, Nigoghossian E, Okach L, Oommachen S, Paulsen J, Reyes R, Rife CL, Trout CV, van den Bedem H, Weekes D, White A, Wolf G, Zubieta C, Hodgson KO, Wooley J, Deacon AM, Godzik A, Lesley SA, Wilson IA. Structural basis of murein peptide specificity of a gamma-D-glutamyl-l-diamino acid endopeptidase. Structure. 2009 Feb 13; 17(2):303-13. PMID: 19217401.
        View in: PubMed
      128. Nair R, Liu J, Soong TT, Acton TB, Everett JK, Kouranov A, Fiser A, Godzik A, Jaroszewski L, Orengo C, Montelione GT, Rost B. Structural genomics is the largest contributor of novel structural leverage. J Struct Funct Genomics. 2009 Apr; 10(2):181-91. PMID: 19194785.
        View in: PubMed
      129. Jaroszewski L, Slabinski L, Wooley J, Deacon AM, Lesley SA, Wilson IA, Godzik A. Genome pool strategy for structural coverage of protein families. Structure. 2008 Nov 12; 16(11):1659-67. PMID: 19000818.
        View in: PubMed
      130. Xu Q, McMullan D, Abdubek P, Astakhova T, Carlton D, Chen C, Chiu HJ, Clayton T, Das D, Deller MC, Duan L, Elsliger MA, Feuerhelm J, Hale J, Han GW, Jaroszewski L, Jin KK, Johnson HA, Klock HE, Knuth MW, Kozbial P, Sri Krishna S, Kumar A, Marciano D, Miller MD, Morse AT, Nigoghossian E, Nopakun A, Okach L, Oommachen S, Paulsen J, Puckett C, Reyes R, Rife CL, Sefcovic N, Trame C, van den Bedem H, Weekes D, Hodgson KO, Wooley J, Deacon AM, Godzik A, Lesley SA, Wilson IA. A structural basis for the regulatory inactivation of DnaA. J Mol Biol. 2009 Jan 16; 385(2):368-80. PMID: 19000695.
        View in: PubMed
      131. Verberkmoes NC, Russell AL, Shah M, Godzik A, Rosenquist M, Halfvarson J, Lefsrud MG, Apajalahti J, Tysk C, Hettich RL, Jansson JK. Shotgun metaproteomics of the human distal gut microbiota. ISME J. 2009 Feb; 3(2):179-89. PMID: 18971961.
        View in: PubMed
      132. Li W, Wooley JC, Godzik A. Probing metagenomics by rapid cluster analysis of very large datasets. PLoS One. 2008; 3(10):e3375. PMID: 18846219; PMCID: PMC2557142.
      133. Igarashi Y, Heureux E, Doctor KS, Talwar P, Gramatikova S, Gramatikoff K, Zhang Y, Blinov M, Ibragimova SS, Boyd S, Ratnikov B, Cieplak P, Godzik A, Smith JW, Osterman AL, Eroshkin AM. PMAP: databases for analyzing proteolytic events and pathways. Nucleic Acids Res. 2009 Jan; 37(Database issue):D611-8. PMID: 18842634; PMCID: PMC2686432.
      134. Veeramalai M, Ye Y, Godzik A. TOPS++FATCAT: fast flexible structural alignment using constraints derived from TOPS+ Strings Model. BMC Bioinformatics. 2008 Aug 31; 9:358. PMID: 18759993; PMCID: PMC2553092.
      135. Zhang Q, Zmasek CM, Dishaw LJ, Mueller MG, Ye Y, Litman GW, Godzik A. Novel genes dramatically alter regulatory network topology in amphioxus. Genome Biol. 2008; 9(8):R123. PMID: 18680598; PMCID: PMC2575513.
      136. Le Negrate G, Krieg A, Faustin B, Loeffler M, Godzik A, Krajewski S, Reed JC. ChlaDub1 of Chlamydia trachomatis suppresses NF-kappaB activation and inhibits IkappaBalpha ubiquitination and degradation. Cell Microbiol. 2008 Sep; 10(9):1879-92. PMID: 18503636.
        View in: PubMed
      137. Holland LZ, Albalat R, Azumi K, Benito-Gutiérrez E, Blow MJ, Bronner-Fraser M, Brunet F, Butts T, Candiani S, Dishaw LJ, Ferrier DE, Garcia-Fernàndez J, Gibson-Brown JJ, Gissi C, Godzik A, Hallböök F, Hirose D, Hosomichi K, Ikuta T, Inoko H, Kasahara M, Kasamatsu J, Kawashima T, Kimura A, Kobayashi M, Kozmik Z, Kubokawa K, Laudet V, Litman GW, McHardy AC, Meulemans D, Nonaka M, Olinski RP, Pancer Z, Pennacchio LA, Pestarino M, Rast JP, Rigoutsos I, Robinson-Rechavi M, Roch G, Saiga H, Sasakura Y, Satake M, Satou Y, Schubert M, Sherwood N, Shiina T, Takatori N, Tello J, Vopalensky P, Wada S, Xu A, Ye Y, Yoshida K, Yoshizaki F, Yu JK, Zhang Q, Zmasek CM, de Jong PJ, Osoegawa K, Putnam NH, Rokhsar DS, Satoh N, Holland PW. The amphioxus genome illuminates vertebrate origins and cephalochordate biology. Genome Res. 2008 Jul; 18(7):1100-11. PMID: 18562680.
        View in: PubMed
      138. Xu Q, Kozbial P, McMullan D, Krishna SS, Brittain SM, Ficarro SB, DiDonato M, Miller MD, Abdubek P, Axelrod HL, Chiu HJ, Clayton T, Duan L, Elsliger MA, Feuerhelm J, Grzechnik SK, Hale J, Han GW, Jaroszewski L, Klock HE, Morse AT, Nigoghossian E, Paulsen J, Reyes R, Rife CL, van den Bedem H, White A, Hodgson KO, Wooley J, Deacon AM, Godzik A, Lesley SA, Wilson IA. Crystal structure of an ADP-ribosylated protein with a cytidine deaminase-like fold, but unknown function (TM1506), from Thermotoga maritima at 2.70 A resolution. Proteins. 2008 May 15; 71(3):1546-52. PMID: 18275082.
        View in: PubMed
      139. Kozbial P, Xu Q, Chiu HJ, McMullan D, Krishna SS, Miller MD, Abdubek P, Acosta C, Astakhova T, Axelrod HL, Carlton D, Clayton T, Deller M, Duan L, Elias Y, Elsliger MA, Feuerhelm J, Grzechnik SK, Hale J, Han GW, Jaroszewski L, Jin KK, Klock HE, Knuth MW, Koesema E, Kumar A, Marciano D, Morse AT, Murphy KD, Nigoghossian E, Okach L, Oommachen S, Reyes R, Rife CL, Spraggon G, Trout CV, van den Bedem H, Weekes D, White A, Wolf G, Zubieta C, Hodgson KO, Wooley J, Deacon AM, Godzik A, Lesley SA, Wilson IA. Crystal structures of MW1337R and lin2004: representatives of a novel protein family that adopt a four-helical bundle fold. Proteins. 2008 May 15; 71(3):1589-96. PMID: 18324683.
        View in: PubMed
      140. Axelrod HL, McMullan D, Krishna SS, Miller MD, Elsliger MA, Abdubek P, Ambing E, Astakhova T, Carlton D, Chiu HJ, Clayton T, Duan L, Feuerhelm J, Grzechnik SK, Hale J, Han GW, Haugen J, Jaroszewski L, Jin KK, Klock HE, Knuth MW, Koesema E, Morse AT, Nigoghossian E, Okach L, Oommachen S, Paulsen J, Quijano K, Reyes R, Rife CL, van den Bedem H, Weekes D, White A, Wolf G, Xu Q, Hodgson KO, Wooley J, Deacon AM, Godzik A, Lesley SA, Wilson IA. Crystal structure of AICAR transformylase IMP cyclohydrolase (TM1249) from Thermotoga maritima at 1.88 A resolution. Proteins. 2008 May 1; 71(2):1042-9. PMID: 18260100.
        View in: PubMed
      141. Le Negrate G, Faustin B, Welsh K, Loeffler M, Krajewska M, Hasegawa P, Mukherjee S, Orth K, Krajewski S, Godzik A, Guiney DG, Reed JC. Salmonella secreted factor L deubiquitinase of Salmonella typhimurium inhibits NF-kappaB, suppresses IkappaBalpha ubiquitination and modulates innate immune responses. J Immunol. 2008 Apr 1; 180(7):5045-56. PMID: 18354230.
        View in: PubMed
      142. Ting JP, Lovering RC, Alnemri ES, Bertin J, Boss JM, Davis BK, Flavell RA, Girardin SE, Godzik A, Harton JA, Hoffman HM, Hugot JP, Inohara N, Mackenzie A, Maltais LJ, Nunez G, Ogura Y, Otten LA, Philpott D, Reed JC, Reith W, Schreiber S, Steimle V, Ward PA. The NLR gene family: a standard nomenclature. Immunity. 2008 Mar; 28(3):285-7. PMID: 18341998; PMCID: PMC2630772.
      143. Mathews II, McMullan D, Miller MD, Canaves JM, Elsliger MA, Floyd R, Grzechnik SK, Jaroszewski L, Klock HE, Koesema E, Kovarik JS, Kreusch A, Kuhn P, McPhillips TM, Morse AT, Quijano K, Rife CL, Schwarzenbacher R, Spraggon G, Stevens RC, van den Bedem H, Weekes D, Wolf G, Hodgson KO, Wooley J, Deacon AM, Godzik A, Lesley SA, Wilson IA. Crystal structure of 2-keto-3-deoxygluconate kinase (TM0067) from Thermotoga maritima at 2.05 A resolution. Proteins. 2008 Feb 1; 70(2):603-8. PMID: 18004772.
        View in: PubMed
      144. Schwarzenbacher R, Godzik A, Jaroszewski L. The JCSG MR pipeline: optimized alignments, multiple models and parallel searches. Acta Crystallogr D Biol Crystallogr. 2008 Jan; 64(Pt 1):133-40. PMID: 18094477.
        View in: PubMed
      145. Krishna SS, Tautz L, Xu Q, McMullan D, Miller MD, Abdubek P, Ambing E, Astakhova T, Axelrod HL, Carlton D, Chiu HJ, Clayton T, DiDonato M, Duan L, Elsliger MA, Grzechnik SK, Hale J, Hampton E, Han GW, Haugen J, Jaroszewski L, Jin KK, Klock HE, Knuth MW, Koesema E, Morse AT, Mustelin T, Nigoghossian E, Oommachen S, Reyes R, Rife CL, van den Bedem H, Weekes D, White A, Hodgson KO, Wooley J, Deacon AM, Godzik A, Lesley SA, Wilson IA. Crystal structure of NMA1982 from Neisseria meningitidis at 1.5 angstroms resolution provides a structural scaffold for nonclassical, eukaryotic-like phosphatases. Proteins. 2007 Nov 1; 69(2):415-21. PMID: 17636569.
        View in: PubMed
      146. Zubieta C, Krishna SS, Kapoor M, Kozbial P, McMullan D, Axelrod HL, Miller MD, Abdubek P, Ambing E, Astakhova T, Carlton D, Chiu HJ, Clayton T, Deller MC, Duan L, Elsliger MA, Feuerhelm J, Grzechnik SK, Hale J, Hampton E, Han GW, Jaroszewski L, Jin KK, Klock HE, Knuth MW, Kumar A, Marciano D, Morse AT, Nigoghossian E, Okach L, Oommachen S, Reyes R, Rife CL, Schimmel P, van den Bedem H, Weekes D, White A, Xu Q, Hodgson KO, Wooley J, Deacon AM, Godzik A, Lesley SA, Wilson IA. Crystal structures of two novel dye-decolorizing peroxidases reveal a beta-barrel fold with a conserved heme-binding motif. Proteins. 2007 Nov 1; 69(2):223-33. PMID: 17654545.
        View in: PubMed
      147. Zubieta C, Joseph R, Krishna SS, McMullan D, Kapoor M, Axelrod HL, Miller MD, Abdubek P, Acosta C, Astakhova T, Carlton D, Chiu HJ, Clayton T, Deller MC, Duan L, Elias Y, Elsliger MA, Feuerhelm J, Grzechnik SK, Hale J, Han GW, Jaroszewski L, Jin KK, Klock HE, Knuth MW, Kozbial P, Kumar A, Marciano D, Morse AT, Murphy KD, Nigoghossian E, Okach L, Oommachen S, Reyes R, Rife CL, Schimmel P, Trout CV, van den Bedem H, Weekes D, White A, Xu Q, Hodgson KO, Wooley J, Deacon AM, Godzik A, Lesley SA, Wilson IA. Identification and structural characterization of heme binding in a novel dye-decolorizing peroxidase, TyrA. Proteins. 2007 Nov 1; 69(2):234-43. PMID: 17654547.
        View in: PubMed
      148. Xu Q, Saikatendu KS, Krishna SS, McMullan D, Abdubek P, Agarwalla S, Ambing E, Astakhova T, Axelrod HL, Carlton D, Chiu HJ, Clayton T, DiDonato M, Duan L, Elsliger MA, Feuerhelm J, Grzechnik SK, Hale J, Hampton E, Han GW, Haugen J, Jaroszewski L, Jin KK, Klock HE, Knuth MW, Koesema E, Miller MD, Morse AT, Nigoghossian E, Okach L, Oommachen S, Paulsen J, Reyes R, Rife CL, Schwarzenbacher R, van den Bedem H, White A, Wolf G, Hodgson KO, Wooley J, Deacon AM, Godzik A, Lesley SA, Wilson IA. Crystal structure of MtnX phosphatase from Bacillus subtilis at 2.0 angstroms resolution provides a structural basis for bipartite phosphomonoester hydrolysis of 2-hydroxy-3-keto-5-methylthiopentenyl-1-phosphate. Proteins. 2007 Nov 1; 69(2):433-9. PMID: 17654724.
        View in: PubMed
      149. Slabinski L, Jaroszewski L, Rodrigues AP, Rychlewski L, Wilson IA, Lesley SA, Godzik A. The challenge of protein structure determination--lessons from structural genomics. Protein Sci. 2007 Nov; 16(11):2472-82. PMID: 17962404.
        View in: PubMed
      150. Slabinski L, Jaroszewski L, Rychlewski L, Wilson IA, Lesley SA, Godzik A. XtalPred: a web server for prediction of protein crystallizability. Bioinformatics. 2007 Dec 15; 23(24):3403-5. PMID: 17921170.
        View in: PubMed
      151. Godzik A, Jambon M, Friedberg I. Computational protein function prediction: are we making progress? Cell Mol Life Sci. 2007 Oct; 64(19-20):2505-11. PMID: 17611711.
        View in: PubMed
      152. Zubieta C, Krishna SS, McMullan D, Miller MD, Abdubek P, Agarwalla S, Ambing E, Astakhova T, Axelrod HL, Carlton D, Chiu HJ, Clayton T, Deller M, DiDonato M, Duan L, Elsliger MA, Grzechnik SK, Hale J, Hampton E, Han GW, Haugen J, Jaroszewski L, Jin KK, Klock HE, Knuth MW, Koesema E, Kumar A, Marciano D, Morse AT, Nigoghossian E, Oommachen S, Reyes R, Rife CL, van den Bedem H, Weekes D, White A, Xu Q, Hodgson KO, Wooley J, Deacon AM, Godzik A, Lesley SA, Wilson IA. Crystal structure of homoserine O-succinyltransferase from Bacillus cereus at 2.4 A resolution. Proteins. 2007 Sep 1; 68(4):999-1005. PMID: 17546672.
        View in: PubMed
      153. Zhang Y, Stec B, Godzik A. Between order and disorder in protein structures: analysis of "dual personality" fragments in proteins. Structure. 2007 Sep; 15(9):1141-7. PMID: 17850753; PMCID: PMC2084070.
      154. Premkumar L, Rife CL, Sri Krishna S, McMullan D, Miller MD, Abdubek P, Ambing E, Astakhova T, Axelrod HL, Canaves JM, Carlton D, Chiu HJ, Clayton T, DiDonato M, Duan L, Elsliger MA, Feuerhelm J, Floyd R, Grzechnik SK, Hale J, Hampton E, Han GW, Haugen J, Jaroszewski L, Jin KK, Klock HE, Knuth MW, Koesema E, Kovarik JS, Kreusch A, Levin I, McPhillips TM, Morse AT, Nigoghossian E, Okach L, Oommachen S, Paulsen J, Quijano K, Reyes R, Rezezadeh F, Rodionov D, Schwarzenbacher R, Spraggon G, van den Bedem H, White A, Wolf G, Xu Q, Hodgson KO, Wooley J, Deacon AM, Godzik A, Lesley SA, Wilson IA. Crystal structure of TM1030 from Thermotoga maritima at 2.3 A resolution reveals molecular details of its transcription repressor function. Proteins. 2007 Jul 1; 68(1):418-24. PMID: 17444523.
        View in: PubMed
      155. Rodrigues AP, Grant BJ, Godzik A, Friedberg I. The 2006 automated function prediction meeting. BMC Bioinformatics. 2007 May 22; 8 Suppl 4:S1-4. PMID: 17570143; PMCID: PMC1892079.
      156. Friedberg I, Nika K, Tautz L, Saito K, Cerignoli F, Friedberg I, Godzik A, Mustelin T. Identification and characterization of DUSP27, a novel dual-specific protein phosphatase. FEBS Lett. 2007 May 29; 581(13):2527-33. PMID: 17498703.
        View in: PubMed
      157. Friedberg I, Godzik A. Functional differentiation of proteins: implications for structural genomics. Structure. 2007 Apr; 15(4):405-15. PMID: 17437713.
        View in: PubMed
      158. Weekes D, Miller MD, Krishna SS, McMullan D, McPhillips TM, Acosta C, Canaves JM, Elsliger MA, Floyd R, Grzechnik SK, Jaroszewski L, Klock HE, Koesema E, Kovarik JS, Kreusch A, Morse AT, Quijano K, Spraggon G, van den Bedem H, Wolf G, Hodgson KO, Wooley J, Deacon AM, Godzik A, Lesley SA, Wilson IA. Crystal structure of a transcription regulator (TM1602) from Thermotoga maritima at 2.3 A resolution. Proteins. 2007 Apr 1; 67(1):247-52. PMID: 17256761.
        View in: PubMed
      159. Grynberg M, Li Z, Szczurek E, Godzik A. Putative type IV secretion genes in Bacillus anthracis. Trends Microbiol. 2007 May; 15(5):191-5. PMID: 17387016.
        View in: PubMed
      160. Yooseph S, Sutton G, Rusch DB, Halpern AL, Williamson SJ, Remington K, Eisen JA, Heidelberg KB, Manning G, Li W, Jaroszewski L, Cieplak P, Miller CS, Li H, Mashiyama ST, Joachimiak MP, van Belle C, Chandonia JM, Soergel DA, Zhai Y, Natarajan K, Lee S, Raphael BJ, Bafna V, Friedman R, Brenner SE, Godzik A, Eisenberg D, Dixon JE, Taylor SS, Strausberg RL, Frazier M, Venter JC. The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families. PLoS Biol. 2007 Mar; 5(3):e16. PMID: 17355171.
        View in: PubMed
      161. Friedberg I, Harder T, Kolodny R, Sitbon E, Li Z, Godzik A. Using an alignment of fragment strings for comparing protein structures. Bioinformatics. 2007 Jan 15; 23(2):e219-24. PMID: 17237095.
        View in: PubMed
      162. Sasin JM, Godzik A, Bujnicki JM. SURF'S UP! - protein classification by surface comparisons. J Biosci. 2007 Jan; 32(1):97-100. PMID: 17426383.
        View in: PubMed
      163. Zmasek CM, Zhang Q, Ye Y, Godzik A. Surprising complexity of the ancestral apoptosis network. Genome Biol. 2007; 8(10):R226. PMID: 17958905; PMCID: PMC2246300.
      164. Igarashi Y, Eroshkin A, Gramatikova S, Gramatikoff K, Zhang Y, Smith JW, Osterman AL, Godzik A. CutDB: a proteolytic event database. Nucleic Acids Res. 2007 Jan; 35(Database issue):D546-9. PMID: 17142225; PMCID: PMC1669773.
      165. Kosloff M, Han GW, Krishna SS, Schwarzenbacher R, Fasnacht M, Elsliger MA, Abdubek P, Agarwalla S, Ambing E, Astakhova T, Axelrod HL, Canaves JM, Carlton D, Chiu HJ, Clayton T, DiDonato M, Duan L, Feuerhelm J, Grittini C, Grzechnik SK, Hale J, Hampton E, Haugen J, Jaroszewski L, Jin KK, Johnson H, Klock HE, Knuth MW, Koesema E, Kreusch A, Kuhn P, Levin I, McMullan D, Miller MD, Morse AT, Moy K, Nigoghossian E, Okach L, Oommachen S, Page R, Paulsen J, Quijano K, Reyes R, Rife CL, Sims E, Spraggon G, Sridhar V, Stevens RC, van den Bedem H, Velasquez J, White A, Wolf G, Xu Q, Hodgson KO, Wooley J, Deacon AM, Godzik A, Lesley SA, Wilson IA. Comparative structural analysis of a novel glutathioneS-transferase (ATU5508) from Agrobacterium tumefaciens at 2.0 A resolution. Proteins. 2006 Nov 15; 65(3):527-37. PMID: 16988933.
        View in: PubMed
      166. DiDonato M, Krishna SS, Schwarzenbacher R, McMullan D, Agarwalla S, Brittain SM, Miller MD, Abdubek P, Ambing E, Axelrod HL, Canaves JM, Chiu HJ, Deacon AM, Duan L, Elsliger MA, Godzik A, Grzechnik SK, Hale J, Hampton E, Haugen J, Jaroszewski L, Jin KK, Klock HE, Knuth MW, Koesema E, Kreusch A, Kuhn P, Lesley SA, Levin I, Morse AT, Nigoghossian E, Okach L, Oommachen S, Paulsen J, Quijano K, Reyes R, Rife CL, Spraggon G, Stevens RC, van den Bedem H, White A, Wolf G, Xu Q, Hodgson KO, Wooley J, Wilson IA. Crystal structure of 2-phosphosulfolactate phosphatase (ComB) from Clostridium acetobutylicum at 2.6 A resolution reveals a new fold with a novel active site. Proteins. 2006 Nov 15; 65(3):771-6. PMID: 16927339.
        View in: PubMed
      167. Xu Q, Krishna SS, McMullan D, Schwarzenbacher R, Miller MD, Abdubek P, Agarwalla S, Ambing E, Astakhova T, Axelrod HL, Canaves JM, Carlton D, Chiu HJ, Clayton T, DiDonato M, Duan L, Elsliger MA, Feuerhelm J, Grzechnik SK, Hale J, Hampton E, Han GW, Haugen J, Jaroszewski L, Jin KK, Klock HE, Knuth MW, Koesema E, Kreusch A, Kuhn P, Morse AT, Nigoghossian E, Okach L, Oommachen S, Paulsen J, Quijano K, Reyes R, Rife CL, Spraggon G, Stevens RC, van den Bedem H, White A, Wolf G, Hodgson KO, Wooley J, Deacon AM, Godzik A, Lesley SA, Wilson IA. Crystal structure of an ORFan protein (TM1622) from Thermotoga maritima at 1.75 A resolution reveals a fold similar to the Ran-binding protein Mog1p. Proteins. 2006 Nov 15; 65(3):777-82. PMID: 16948158.
        View in: PubMed
      168. Zhi D, Krishna SS, Cao H, Pevzner P, Godzik A. Representing and comparing protein structures as paths in three-dimensional space. BMC Bioinformatics. 2006; 7:460. PMID: 17052359.
        View in: PubMed
      169. Awobuluyi M, Yang J, Ye Y, Chatterton JE, Godzik A, Lipton SA, Zhang D. Subunit-specific roles of glycine-binding domains in activation of NR1/NR3 N-methyl-D-aspartate receptors. Mol Pharmacol. 2007 Jan; 71(1):112-22. PMID: 17047094.
        View in: PubMed
      170. Ginalski K, Godzik A, Rychlewski L. Novel SARS unique AdoMet-dependent methyltransferase. Cell Cycle. 2006 Oct; 5(20):2414-6. PMID: 17102613.
        View in: PubMed
      171. Schwarzenbacher R, McMullan D, Krishna SS, Xu Q, Miller MD, Canaves JM, Elsliger MA, Floyd R, Grzechnik SK, Jaroszewski L, Klock HE, Koesema E, Kovarik JS, Kreusch A, Kuhn P, McPhillips TM, Morse AT, Quijano K, Spraggon G, Stevens RC, van den Bedem H, Wolf G, Hodgson KO, Wooley J, Deacon AM, Godzik A, Lesley SA, Wilson IA. Crystal structure of a glycerate kinase (TM1585) from Thermotoga maritima at 2.70 A resolution reveals a new fold. Proteins. 2006 Oct 1; 65(1):243-8. PMID: 16865707.
        View in: PubMed
      172. Mathews II, Krishna SS, Schwarzenbacher R, McMullan D, Jaroszewski L, Miller MD, Abdubek P, Agarwalla S, Ambing E, Axelrod HL, Canaves JM, Carlton D, Chiu HJ, Clayton T, DiDonato M, Duan L, Elsliger MA, Grzechnik SK, Hale J, Hampton E, Haugen J, Jin KK, Klock HE, Koesema E, Kovarik JS, Kreusch A, Kuhn P, Levin I, Morse AT, Nigoghossian E, Okach L, Oommachen S, Paulsen J, Quijano K, Reyes R, Rife CL, Spraggon G, Stevens RC, van den Bedem H, White A, Wolf G, Xu Q, Hodgson KO, Wooley J, Deacon AM, Godzik A, Lesley SA, Wilson IA. Crystal structure of phosphoribosylformyl-glycinamidine synthase II, PurS subunit (TM1244) from Thermotoga maritima at 1.90 A resolution. Proteins. 2006 Oct 1; 65(1):249-54. PMID: 16865708.
        View in: PubMed
      173. White AK, Hoch JA, Grynberg M, Godzik A, Perego M. Sensor domains encoded in Bacillus anthracis virulence plasmids prevent sporulation by hijacking a sporulation sensor histidine kinase. J Bacteriol. 2006 Sep; 188(17):6354-60. PMID: 16923903; PMCID: PMC1595385.
      174. Han GW, Sri Krishna S, Schwarzenbacher R, McMullan D, Ginalski K, Elsliger MA, Brittain SM, Abdubek P, Agarwalla S, Ambing E, Astakhova T, Axelrod H, Canaves JM, Chiu HJ, DiDonato M, Grzechnik SK, Hale J, Hampton E, Haugen J, Jaroszewski L, Jin KK, Klock HE, Knuth MW, Koesema E, Kreusch A, Kuhn P, Miller MD, Morse AT, Moy K, Nigoghossian E, Oommachen S, Ouyang J, Paulsen J, Quijano K, Reyes R, Rife C, Spraggon G, Stevens RC, van den Bedem H, Velasquez J, Wang X, West B, White A, Wolf G, Xu Q, Hodgson KO, Wooley J, Deacon AM, Godzik A, Lesley SA, Wilson IA. Crystal structure of the ApbE protein (TM1553) from Thermotoga maritima at 1.58 A resolution. Proteins. 2006 Sep 1; 64(4):1083-90. PMID: 16779835.
        View in: PubMed
      175. Xu Q, Schwarzenbacher R, Krishna SS, McMullan D, Agarwalla S, Quijano K, Abdubek P, Ambing E, Axelrod H, Biorac T, Canaves JM, Chiu HJ, Elsliger MA, Grittini C, Grzechnik SK, DiDonato M, Hale J, Hampton E, Han GW, Haugen J, Hornsby M, Jaroszewski L, Klock HE, Knuth MW, Koesema E, Kreusch A, Kuhn P, Miller MD, Moy K, Nigoghossian E, Paulsen J, Reyes R, Rife C, Spraggon G, Stevens RC, van den Bedem H, Velasquez J, White A, Wolf G, Hodgson KO, Wooley J, Deacon AM, Godzik A, Lesley SA, Wilson IA. Crystal structure of acireductone dioxygenase (ARD) from Mus musculus at 2.06 angstrom resolution. Proteins. 2006 Aug 15; 64(3):808-13. PMID: 16783794.
        View in: PubMed
      176. Friedberg I, Harder T, Godzik A. JAFA: a protein function annotation meta-server. Nucleic Acids Res. 2006 Jul 01; 34(Web Server issue):W379-81. PMID: 16845030; PMCID: PMC1538919.
      177. Friedberg I, Jambon M, Godzik A. New avenues in protein function prediction. Protein Sci. 2006 Jun; 15(6):1527-9. PMID: 16731984; PMCID: PMC2242544.
      178. Jin KK, Krishna SS, Schwarzenbacher R, McMullan D, Abdubek P, Agarwalla S, Ambing E, Axelrod H, Canaves JM, Chiu HJ, Deacon AM, DiDonato M, Elsliger MA, Feuerhelm J, Godzik A, Grittini C, Grzechnik SK, Hale J, Hampton E, Haugen J, Hornsby M, Jaroszewski L, Klock HE, Knuth MW, Koesema E, Kreusch A, Kuhn P, Lesley SA, Miller MD, Moy K, Nigoghossian E, Okach L, Oommachen S, Paulsen J, Quijano K, Reyes R, Rife C, Stevens RC, Spraggon G, van den Bedem H, Velasquez J, White A, Wolf G, Han GW, Xu Q, Hodgson KO, Wooley J, Wilson IA. Crystal structure of TM1367 from Thermotoga maritima at 1.90 A resolution reveals an atypical member of the cyclophilin (peptidylprolyl isomerase) fold. Proteins. 2006 Jun 1; 63(4):1112-8. PMID: 16544291.
        View in: PubMed
      179. Mathews II, Krishna SS, Schwarzenbacher R, McMullan D, Abdubek P, Ambing E, Canaves JM, Chiu HJ, Deacon AM, DiDonato M, Elsliger MA, Godzik A, Grittini C, Grzechnik SK, Hale J, Hampton E, Han GW, Haugen J, Jaroszewski L, Klock HE, Koesema E, Kreusch A, Kuhn P, Lesley SA, Levin I, Miller MD, Moy K, Nigoghossian E, Paulsen J, Quijano K, Reyes R, Spraggon G, Stevens RC, van den Bedem H, Velasquez J, White A, Wolf G, Xu Q, Hodgson KO, Wooley J, Wilson IA. Crystal structure of phosphoribosylformylglycinamidine synthase II (smPurL) from Thermotoga maritima at 2.15 A resolution. Proteins. 2006 Jun 1; 63(4):1106-11. PMID: 16544324.
        View in: PubMed
      180. Li W, Godzik A. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics. 2006 Jul 01; 22(13):1658-9. PMID: 16731699.
        View in: PubMed
      181. Doukhanina EV, Chen S, van der Zalm E, Godzik A, Reed J, Dickman MB. Identification and functional characterization of the BAG protein family in Arabidopsis thaliana. J Biol Chem. 2006 Jul 07; 281(27):18793-801. PMID: 16636050.
        View in: PubMed
      182. DiDonato M, Krishna SS, Schwarzenbacher R, McMullan D, Jaroszewski L, Miller MD, Abdubek P, Agarwalla S, Ambing E, Axelrod H, Biorac T, Chiu HJ, Deacon AM, Elsliger MA, Feuerhelm J, Godzik A, Grittini C, Grzechnik SK, Hale J, Hampton E, Haugen J, Hornsby M, Klock HE, Knuth MW, Koesema E, Kreusch A, Kuhn P, Lesley SA, Moy K, Nigoghossian E, Okach L, Paulsen J, Quijano K, Reyes R, Rife C, Spraggon G, Stevens RC, van den Bedem H, Velasquez J, White A, Wolf G, Xu Q, Hodgson KO, Wooley J, Wilson IA. Crystal structure of a single-stranded DNA-binding protein (TM0604) from Thermotoga maritima at 2.60 A resolution. Proteins. 2006 Apr 1; 63(1):256-60. PMID: 16435371.
        View in: PubMed
      183. Li W, Godzik A. VISSA: a program to visualize structural features from structure sequence alignment. Bioinformatics. 2006 Apr 01; 22(7):887-8. PMID: 16434438.
        View in: PubMed
      184. Shiryaev SA, Ratnikov BI, Chekanov AV, Sikora S, Rozanov DV, Godzik A, Wang J, Smith JW, Huang Z, Lindberg I, Samuel MA, Diamond MS, Strongin AY. Cleavage targets and the D-arginine-based inhibitors of the West Nile virus NS3 processing proteinase. Biochem J. 2006 Jan 15; 393(Pt 2):503-11. PMID: 16229682; PMCID: PMC1360700.
      185. Ye Y, Li Z, Godzik A. Modeling and analyzing three-dimensional structures of human disease proteins. Pac Symp Biocomput. 2006; 439-50. PMID: 17094259.
        View in: PubMed
      186. Li Z, Ye Y, Godzik A. Flexible Structural Neighborhood--a database of protein structural similarities and alignments. Nucleic Acids Res. 2006 Jan 01; 34(Database issue):D277-80. PMID: 16381864; PMCID: PMC1347486.
      187. Newman RM, Salunkhe P, Godzik A, Reed JC. Identification and characterization of a novel bacterial virulence factor that shares homology with mammalian Toll/interleukin-1 receptor family proteins. Infect Immun. 2006 Jan; 74(1):594-601. PMID: 16369016; PMCID: PMC1346628.
      188. Xu Q, Schwarzenbacher R, McMullan D, Abdubek P, Agarwalla S, Ambing E, Axelrod H, Biorac T, Canaves JM, Chiu HJ, Deacon AM, DiDonato M, Elsliger MA, Godzik A, Grittini C, Grzechnik SK, Hale J, Hampton E, Han GW, Haugen J, Hornsby M, Jaroszewski L, Klock HE, Koesema E, Kreusch A, Kuhn P, Lesley SA, Miller MD, Moy K, Nigoghossian E, Paulsen J, Quijano K, Reyes R, Rife C, Spraggon G, Stevens RC, van den Bedem H, Velasquez J, White A, Wolf G, Hodgson KO, Wooley J, Wilson IA. Crystal structure of virulence factor CJ0248 from Campylobacter jejuni at 2.25 A resolution reveals a new fold. Proteins. 2006 Jan 1; 62(1):292-6. PMID: 16287129.
        View in: PubMed
      189. Plewczynski D, Tkacz A, Wyrwicz LS, Godzik A, Kloczkowski A, Rychlewski L. Support-vector-machine classification of linear functional motifs in proteins. J Mol Model. 2006 Mar; 12(4):453-61. PMID: 16341901.
        View in: PubMed
      190. Robinson-Rechavi M, Alibés A, Godzik A. Contribution of electrostatic interactions, compactness and quaternary structure to protein thermostability: lessons from structural genomics of Thermotoga maritima. J Mol Biol. 2006 Feb 17; 356(2):547-57. PMID: 16375925.
        View in: PubMed
      191. Klock HE, Schwarzenbacher R, Xu Q, McMullan D, Abdubek P, Ambing E, Axelrod H, Biorac T, Canaves JM, Chiu HJ, Deacon AM, DiDonato M, Elsliger MA, Godzik A, Grittini C, Grzechnik SK, Hale J, Hampton E, Han GW, Haugen J, Hornsby M, Jaroszewski L, Koesema E, Kreusch A, Kuhn P, Miller MD, Moy K, Nigoghossian E, Paulsen J, Quijano K, Reyes R, Rife C, Sims E, Spraggon G, Stevens RC, van den Bedem H, Velasquez J, Vincent J, White A, Wolf G, Hodgson KO, Wooley J, Lesley SA, Wilson IA. Crystal structure of a conserved hypothetical protein (gi: 13879369) from Mouse at 1.90 A resolution reveals a new fold. Proteins. 2005 Dec 1; 61(4):1132-6. PMID: 16224779.
        View in: PubMed
      192. Jaroszewski L, Schwarzenbacher R, McMullan D, Abdubek P, Agarwalla S, Ambing E, Axelrod H, Biorac T, Canaves JM, Chiu HJ, Deacon AM, DiDonato M, Elsliger MA, Godzik A, Grittini C, Grzechnik SK, Hale J, Hampton E, Han GW, Haugen J, Hornsby M, Klock HE, Koesema E, Kreusch A, Kuhn P, Lesley SA, Miller MD, Moy K, Nigoghossian E, Paulsen J, Quijano K, Reyes R, Rife C, Spraggon G, Stevens RC, van den Bedem H, Velasquez J, Vincent J, White A, Wolf G, Xu Q, Hodgson KO, Wooley J, Wilson IA. Crystal structure of Hsp33 chaperone (TM1394) from Thermotoga maritima at 2.20 A resolution. Proteins. 2005 Nov 15; 61(3):669-73. PMID: 16167343.
        View in: PubMed
      193. Rife C, Schwarzenbacher R, McMullan D, Abdubek P, Ambing E, Axelrod H, Biorac T, Canaves JM, Chiu HJ, Deacon AM, DiDonato M, Elsliger MA, Godzik A, Grittini C, Grzechnik SK, Hale J, Hampton E, Han GW, Haugen J, Hornsby M, Jaroszewski L, Klock HE, Koesema E, Kreusch A, Kuhn P, Lesley SA, Miller MD, Moy K, Nigoghossian E, Paulsen J, Quijano K, Reyes R, Sims E, Spraggon G, Stevens RC, van den Bedem H, Velasquez J, Vincent J, White A, Wolf G, Xu Q, Hodgson KO, Wooley J, Wilson IA. Crystal structure of the global regulatory protein CsrA from Pseudomonas putida at 2.05 A resolution reveals a new fold. Proteins. 2005 Nov 1; 61(2):449-53. PMID: 16104018.
        View in: PubMed
      194. Rife C, Schwarzenbacher R, McMullan D, Abdubek P, Ambing E, Axelrod H, Biorac T, Canaves JM, Chiu HJ, Deacon AM, DiDonato M, Elsliger MA, Godzik A, Grittini C, Grzechnik SK, Hale J, Hampton E, Han GW, Haugen J, Hornsby M, Jaroszewski L, Klock HE, Koesema E, Kreusch A, Kuhn P, Lesley SA, Miller MD, Moy K, Nigoghossian E, Paulsen J, Quijano K, Reyes R, Sims E, Spraggon G, Stevens RC, van den Bedem H, Velasquez J, Vincent J, White A, Wolf G, Xu Q, Hodgson KO, Wooley J, Wilson IA. Crystal structure of a putative modulator of DNA gyrase (pmbA) from Thermotoga maritima at 1.95 A resolution reveals a new fold. Proteins. 2005 Nov 1; 61(2):444-8. PMID: 16104019.
        View in: PubMed
      195. Sikora S, Strongin A, Godzik A. Convergent evolution as a mechanism for pathogenic adaptation. Trends Microbiol. 2005 Nov; 13(11):522-7. PMID: 16153847.
        View in: PubMed
      196. Han GW, Schwarzenbacher R, McMullan D, Abdubek P, Ambing E, Axelrod H, Biorac T, Canaves JM, Chiu HJ, Dai X, Deacon AM, DiDonato M, Elsliger MA, Godzik A, Grittini C, Grzechnik SK, Hale J, Hampton E, Haugen J, Hornsby M, Jaroszewski L, Klock HE, Koesema E, Kreusch A, Kuhn P, Lesley SA, McPhillips TM, Miller MD, Moy K, Nigoghossian E, Paulsen J, Quijano K, Reyes R, Spraggon G, Stevens RC, van den Bedem H, Velasquez J, Vincent J, White A, Wolf G, Xu Q, Hodgson KO, Wooley J, Wilson IA. Crystal structure of an Apo mRNA decapping enzyme (DcpS) from Mouse at 1.83 A resolution. Proteins. 2005 Sep 1; 60(4):797-802. PMID: 16001405.
        View in: PubMed
      197. Plewczynski D, Jaroszewski L, Godzik A, Kloczkowski A, Rychlewski L. Molecular modeling of phosphorylation sites in proteins using a database of local structure segments. J Mol Model. 2005 Nov; 11(6):431-8. PMID: 16094535.
        View in: PubMed
      198. Friedberg I, Godzik A. Connecting the protein structure universe by using sparse recurring fragments. Structure. 2005 Aug; 13(8):1213-24. PMID: 16084393.
        View in: PubMed
      199. Friedberg I, Godzik A. Fragnostic: walking through protein structure space. Nucleic Acids Res. 2005 Jul 01; 33(Web Server issue):W249-51. PMID: 15980462; PMCID: PMC1160124.
      200. Jaroszewski L, Rychlewski L, Li Z, Li W, Godzik A. FFAS03: a server for profile--profile sequence alignments. Nucleic Acids Res. 2005 Jul 1; 33(Web Server issue):W284-8. PMID: 15980471.
        View in: PubMed
      201. Levin I, Miller MD, Schwarzenbacher R, McMullan D, Abdubek P, Ambing E, Biorac T, Cambell J, Canaves JM, Chiu HJ, Deacon AM, DiDonato M, Elsliger MA, Godzik A, Grittini C, Grzechnik SK, Hale J, Hampton E, Han GW, Haugen J, Hornsby M, Jaroszewski L, Karlak C, Klock HE, Koesema E, Kreusch A, Kuhn P, Lesley SA, Morse A, Moy K, Nigoghossian E, Ouyang J, Page R, Quijano K, Reyes R, Robb A, Sims E, Spraggon G, Stevens RC, van den Bedem H, Velasquez J, Vincent J, Wang X, West B, Wolf G, Xu Q, Zagnitko O, Hodgson KO, Wooley J, Wilson IA. Crystal structure of an indigoidine synthase A (IndA)-like protein (TM1464) from Thermotoga maritima at 1.90 A resolution reveals a new fold. Proteins. 2005 Jun 1; 59(4):864-8. PMID: 15822122.
        View in: PubMed
      202. Mathews I, Schwarzenbacher R, McMullan D, Abdubek P, Ambing E, Axelrod H, Biorac T, Canaves JM, Chiu HJ, Deacon AM, DiDonato M, Elsliger MA, Godzik A, Grittini C, Grzechnik SK, Hale J, Hampton E, Han GW, Haugen J, Hornsby M, Jaroszewski L, Klock HE, Koesema E, Kreusch A, Kuhn P, Lesley SA, Levin I, Miller MD, Moy K, Nigoghossian E, Ouyang J, Paulsen J, Quijano K, Reyes R, Spraggon G, Stevens RC, van den Bedem H, Velasquez J, Vincent J, White A, Wolf G, Xu Q, Hodgson KO, Wooley J, Wilson IA. Crystal structure of S-adenosylmethionine:tRNA ribosyltransferase-isomerase (QueA) from Thermotoga maritima at 2.0 A resolution reveals a new fold. Proteins. 2005 Jun 1; 59(4):869-74. PMID: 15822125.
        View in: PubMed
      203. Robinson-Rechavi M, Godzik A. Structural genomics of thermotoga maritima proteins shows that contact order is a major determinant of protein thermostability. Structure. 2005 Jun; 13(6):857-60. PMID: 15939017.
        View in: PubMed
      204. Ye Y, Osterman A, Overbeek R, Godzik A. Automatic detection of subsystem/pathway variants in genome analysis. Bioinformatics. 2005 Jun; 21 Suppl 1:i478-86. PMID: 15961494.
        View in: PubMed
      205. Ginalski K, Grishin NV, Godzik A, Rychlewski L. Practical lessons from protein structure prediction. Nucleic Acids Res. 2005; 33(6):1874-91. PMID: 15805122; PMCID: PMC1074308.
      206. Ye Y, Godzik A. Multiple flexible structure alignment using partial order graphs. Bioinformatics. 2005 May 15; 21(10):2362-9. PMID: 15746292.
        View in: PubMed
      207. Xu Q, Schwarzenbacher R, McMullan D, Abdubek P, Ambing E, Biorac T, Canaves JM, Chiu HJ, Dai X, Deacon AM, DiDonato M, Elsliger MA, Godzik A, Grittini C, Grzechnik SK, Hampton E, Hornsby M, Jaroszewski L, Klock HE, Koesema E, Kreusch A, Kuhn P, Lesley SA, Levin I, Miller MD, Morse A, Moy K, Ouyang J, Page R, Quijano K, Reyes R, Robb A, Sims E, Spraggon G, Stevens RC, van den Bedem H, Velasquez J, Vincent J, von Delft F, Wang X, West B, White A, Wolf G, Zagnitko O, Hodgson KO, Wooley J, Wilson IA. Crystal structure of a formiminotetrahydrofolate cyclodeaminase (TM1560) from Thermotoga maritima at 2.80 A resolution reveals a new fold. Proteins. 2005 Mar 1; 58(4):976-81. PMID: 15651027.
        View in: PubMed
      208. Han GW, Schwarzenbacher R, Page R, Jaroszewski L, Abdubek P, Ambing E, Biorac T, Canaves JM, Chiu HJ, Dai X, Deacon AM, DiDonato M, Elsliger MA, Godzik A, Grittini C, Grzechnik SK, Hale J, Hampton E, Haugen J, Hornsby M, Klock HE, Koesema E, Kreusch A, Kuhn P, Lesley SA, Levin I, McMullan D, McPhillips TM, Miller MD, Morse A, Moy K, Nigoghossian E, Ouyang J, Paulsen J, Quijano K, Reyes R, Sims E, Spraggon G, Stevens RC, van den Bedem H, Velasquez J, Vincent J, von Delft F, Wang X, West B, White A, Wolf G, Xu Q, Zagnitko O, Hodgson KO, Wooley J, Wilson IA. Crystal structure of an alanine-glyoxylate aminotransferase from Anabaena sp. at 1.70 A resolution reveals a noncovalently linked PLP cofactor. Proteins. 2005 Mar 1; 58(4):971-5. PMID: 15657930.
        View in: PubMed
      209. Arndt JW, Schwarzenbacher R, Page R, Abdubek P, Ambing E, Biorac T, Canaves JM, Chiu HJ, Dai X, Deacon AM, DiDonato M, Elsliger MA, Godzik A, Grittini C, Grzechnik SK, Hale J, Hampton E, Han GW, Haugen J, Hornsby M, Klock HE, Koesema E, Kreusch A, Kuhn P, Jaroszewski L, Lesley SA, Levin I, McMullan D, McPhillips TM, Miller MD, Morse A, Moy K, Nigoghossian E, Ouyang J, Peti WS, Quijano K, Reyes R, Sims E, Spraggon G, Stevens RC, van den Bedem H, Velasquez J, Vincent J, von Delft F, Wang X, West B, White A, Wolf G, Xu Q, Zagnitko O, Hodgson KO, Wooley J, Wilson IA. Crystal structure of an alpha/beta serine hydrolase (YDR428C) from Saccharomyces cerevisiae at 1.85 A resolution. Proteins. 2005 Feb 15; 58(3):755-8. PMID: 15624212.
        View in: PubMed
      210. Plewczynski D, Tkacz A, Godzik A, Rychlewski L. A support vector machine approach to the identification of phosphorylation sites. Cell Mol Biol Lett. 2005; 10(1):73-89. PMID: 15809681.
        View in: PubMed
      211. Miller MD, Schwarzenbacher R, von Delft F, Abdubek P, Ambing E, Biorac T, Brinen LS, Canaves JM, Cambell J, Chiu HJ, Dai X, Deacon AM, DiDonato M, Elsliger MA, Eshagi S, Floyd R, Godzik A, Grittini C, Grzechnik SK, Hampton E, Jaroszewski L, Karlak C, Klock HE, Koesema E, Kovarik JS, Kreusch A, Kuhn P, Lesley SA, Levin I, McMullan D, McPhillips TM, Morse A, Moy K, Ouyang J, Page R, Quijano K, Robb A, Spraggon G, Stevens RC, van den Bedem H, Velasquez J, Vincent J, Wang X, West B, Wolf G, Xu Q, Hodgson KO, Wooley J, Wilson IA. Crystal structure of a tandem cystathionine-beta-synthase (CBS) domain protein (TM0935) from Thermotoga maritima at 1.87 A resolution. Proteins. 2004 Oct 1; 57(1):213-7. PMID: 15326606.
        View in: PubMed
      212. Rozanov DV, Sikora S, Godzik A, Postnova TI, Golubkov V, Savinov A, Tomlinson S, Strongin AY. Non-proteolytic, receptor/ligand interactions associate cellular membrane type-1 matrix metalloproteinase with the complement component C1q. J Biol Chem. 2004 Nov 26; 279(48):50321-8. PMID: 15375167.
        View in: PubMed
      213. Dodatko T, Fedorov AA, Grynberg M, Patskovsky Y, Rozwarski DA, Jaroszewski L, Aronoff-Spencer E, Kondraskina E, Irving T, Godzik A, Almo SC. Crystal structure of the actin binding domain of the cyclase-associated protein. Biochemistry. 2004 Aug 24; 43(33):10628-41. PMID: 15311924.
        View in: PubMed
      214. Bakolitsa C, Schwarzenbacher R, McMullan D, Brinen LS, Canaves JM, Dai X, Deacon AM, Elsliger MA, Eshagi S, Floyd R, Godzik A, Grittini C, Grzechnik SK, Jaroszewski L, Karlak C, Klock HE, Koesema E, Kovarik JS, Kreusch A, Kuhn P, Lesley SA, McPhillips TM, Miller MD, Morse A, Moy K, Ouyang J, Page R, Quijano K, Robb A, Spraggon G, Stevens RC, van den Bedem H, Velasquez J, Vincent J, von Delft F, Wang X, West B, Wolf G, Hodgson KO, Wooley J, Wilson IA. Crystal structure of an orphan protein (TM0875) from Thermotoga maritima at 2.00-A resolution reveals a new fold. Proteins. 2004 Aug 15; 56(3):607-10. PMID: 15229892.
        View in: PubMed
      215. Jaroszewski L, Schwarzenbacher R, von Delft F, McMullan D, Brinen LS, Canaves JM, Dai X, Deacon AM, DiDonato M, Elsliger MA, Eshagi S, Floyd R, Godzik A, Grittini C, Grzechnik SK, Hampton E, Levin I, Karlak C, Klock HE, Koesema E, Kovarik JS, Kreusch A, Kuhn P, Lesley SA, McPhillips TM, Miller MD, Morse A, Moy K, Ouyang J, Page R, Quijano K, Reyes R, Rezezadeh F, Robb A, Sims E, Spraggon G, Stevens RC, van den Bedem H, Velasquez J, Vincent J, Wang X, West B, Wolf G, Xu Q, Hodgson KO, Wooley J, Wilson IA. Crystal structure of a novel manganese-containing cupin (TM1459) from Thermotoga maritima at 1.65 A resolution. Proteins. 2004 Aug 15; 56(3):611-4. PMID: 15229893.
        View in: PubMed
      216. McMullan D, Schwarzenbacher R, Jaroszewski L, von Delft F, Klock HE, Vincent J, Quijano K, Abdubek P, Ambing E, Biorac T, Brinen LS, Canaves JM, Dai X, Deacon AM, DiDonato M, Elsliger MA, Eshaghi S, Floyd R, Godzik A, Grittini C, Grzechnik SK, Hampton E, Karlak C, Koesema E, Kreusch A, Kuhn P, Levin I, McPhillips TM, Miller MD, Morse A, Moy K, Ouyang J, Page R, Reyes R, Rezezadeh F, Robb A, Sims E, Spraggon G, Stevens RC, van den Bedem H, Velasquez J, Wang X, West B, Wolf G, Xu Q, Hodgson KO, Wooley J, Lesley SA, Wilson IA. Crystal structure of a novel Thermotoga maritima enzyme (TM1112) from the cupin family at 1.83 A resolution. Proteins. 2004 Aug 15; 56(3):615-8. PMID: 15229894.
        View in: PubMed
      217. Xu Q, Schwarzenbacher R, Page R, Sims E, Abdubek P, Ambing E, Biorac T, Brinen LS, Cambell J, Canaves JM, Chiu HJ, Dai X, Deacon AM, DiDonato M, Elsliger MA, Floyd R, Godzik A, Grittini C, Grzechnik SK, Hampton E, Jaroszewski L, Karlak C, Klock HE, Koesema E, Kovarik JS, Kreusch A, Kuhn P, Lesley SA, Levin I, McMullan D, McPhillips TM, Miller MD, Morse A, Moy K, Ouyang J, Quijano K, Reyes R, Rezezadeh F, Robb A, Spraggon G, Stevens RC, van den Bedem H, Velasquez J, Vincent J, von Delft F, Wang X, West B, Wolf G, Hodgson KO, Wooley J, Wilson IA. Crystal structure of an allantoicase (YIR029W) from Saccharomyces cerevisiae at 2.4 A resolution. Proteins. 2004 Aug 15; 56(3):619-24. PMID: 15229895.
        View in: PubMed
      218. Levin I, Schwarzenbacher R, McMullan D, Abdubek P, Ambing E, Biorac T, Cambell J, Canaves JM, Chiu HJ, Dai X, Deacon AM, DiDonato M, Elsliger MA, Godzik A, Grittini C, Grzechnik SK, Hampton E, Jaroszewski L, Karlak C, Klock HE, Koesema E, Kreusch A, Kuhn P, Lesley SA, McPhillips TM, Miller MD, Morse A, Moy K, Ouyang J, Page R, Quijano K, Reyes R, Robb A, Sims E, Spraggon G, Stevens RC, van den Bedem H, Velasquez J, Vincent J, von Delft F, Wang X, West B, Wolf G, Xu Q, Hodgson KO, Wooley J, Wilson IA. Crystal structure of a putative NADPH-dependent oxidoreductase (GI: 18204011) from mouse at 2.10 A resolution. Proteins. 2004 Aug 15; 56(3):629-33. PMID: 15229897.
        View in: PubMed
      219. Heine A, Canaves JM, von Delft F, Brinen LS, Dai X, Deacon AM, Elsliger MA, Eshaghi S, Floyd R, Godzik A, Grittini C, Grzechnik SK, Guda C, Jaroszewski L, Karlak C, Klock HE, Koesema E, Kovarik JS, Kreusch A, Kuhn P, Lesley SA, McMullan D, McPhillips TM, Miller MA, Miller MD, Morse A, Moy K, Ouyang J, Page R, Robb A, Rodrigues K, Schwarzenbacher R, Selby TL, Spraggon G, Stevens RC, van den Bedem H, Velasquez J, Vincent J, Wang X, West B, Wolf G, Hodgson KO, Wooley J, Wilson IA. Crystal structure of O-acetylserine sulfhydrylase (TM0665) from Thermotoga maritima at 1.8 A resolution. Proteins. 2004 Aug 1; 56(2):387-91. PMID: 15211522.
        View in: PubMed
      220. Schwarzenbacher R, von Delft F, Jaroszewski L, Abdubek P, Ambing E, Biorac T, Brinen LS, Canaves JM, Cambell J, Chiu HJ, Dai X, Deacon AM, DiDonato M, Elsliger MA, Eshagi S, Floyd R, Godzik A, Grittini C, Grzechnik SK, Hampton E, Karlak C, Klock HE, Koesema E, Kovarik JS, Kreusch A, Kuhn P, Lesley SA, Levin I, McMullan D, McPhillips TM, Miller MD, Morse A, Moy K, Ouyang J, Page R, Quijano K, Robb A, Spraggon G, Stevens RC, van den Bedem H, Velasquez J, Vincent J, Wang X, West B, Wolf G, Xu Q, Hodgson KO, Wooley J, Wilson IA. Crystal structure of a putative oxalate decarboxylase (TM1287) from Thermotoga maritima at 1.95 A resolution. Proteins. 2004 Aug 1; 56(2):392-5. PMID: 15211523.
        View in: PubMed
      221. Spraggon G, Schwarzenbacher R, Kreusch A, McMullan D, Brinen LS, Canaves JM, Dai X, Deacon AM, Elsliger MA, Eshagi S, Floyd R, Godzik A, Grittini C, Grzechnik SK, Jaroszewski L, Karlak C, Klock HE, Koesema E, Kovarik JS, Kuhn P, McPhillips TM, Miller MD, Morse A, Moy K, Ouyang J, Page R, Quijano K, Rezezadeh F, Robb A, Sims E, Stevens RC, van den Bedem H, Velasquez J, Vincent J, von Delft F, Wang X, West B, Wolf G, Xu Q, Hodgson KO, Wooley J, Lesley SA, Wilson IA. Crystal structure of a methionine aminopeptidase (TM1478) from Thermotoga maritima at 1.9 A resolution. Proteins. 2004 Aug 1; 56(2):396-400. PMID: 15211524.
        View in: PubMed
      222. Levin I, Schwarzenbacher R, Page R, Abdubek P, Ambing E, Biorac T, Brinen LS, Campbell J, Canaves JM, Chiu HJ, Dai X, Deacon AM, DiDonato M, Elsliger MA, Floyd R, Godzik A, Grittini C, Grzechnik SK, Hampton E, Jaroszewski L, Karlak C, Klock HE, Koesema E, Kovarik JS, Kreusch A, Kuhn P, Lesley SA, McMullan D, McPhillips TM, Miller MD, Morse A, Moy K, Ouyang J, Quijano K, Reyes R, Rezezadeh F, Robb A, Sims E, Spraggon G, Stevens RC, van den Bedem H, Velasquez J, Vincent J, von Delft F, Wang X, West B, Wolf G, Xu Q, Hodgson KO, Wooley J, Wilson IA. Crystal structure of a PIN (PilT N-terminus) domain (AF0591) from Archaeoglobus fulgidus at 1.90 A resolution. Proteins. 2004 Aug 1; 56(2):404-8. PMID: 15211526.
        View in: PubMed
      223. Plewczynski D, Rychlewski L, Ye Y, Jaroszewski L, Godzik A. Integrated web service for improving alignment quality based on segments comparison. BMC Bioinformatics. 2004 Jul 22; 5:98. PMID: 15271224.
        View in: PubMed
      224. Santelli E, Schwarzenbacher R, McMullan D, Biorac T, Brinen LS, Canaves JM, Cambell J, Dai X, Deacon AM, Elsliger MA, Eshagi S, Floyd R, Godzik A, Grittini C, Grzechnik SK, Jaroszewski L, Karlak C, Klock HE, Koesema E, Kovarik JS, Kreusch A, Kuhn P, Lesley SA, McPhillips TM, Miller MD, Morse A, Moy K, Ouyang J, Page R, Quijano K, Rezezadeh F, Robb A, Sims E, Spraggon G, Stevens RC, van den Bedem H, Velasquez J, Vincent J, von Delft F, Wang X, West B, Wolf G, Xu Q, Hodgson KO, Wooley J, Wilson IA. Crystal structure of a glycerophosphodiester phosphodiesterase (GDPD) from Thermotoga maritima (TM1621) at 1.60 A resolution. Proteins. 2004 Jul 1; 56(1):167-70. PMID: 15162496.
        View in: PubMed
      225. Xu Q, Schwarzenbacher R, McMullan D, von Delft F, Brinen LS, Canaves JM, Dai X, Deacon AM, Elsliger MA, Eshagi S, Floyd R, Godzik A, Grittini C, Grzechnik SK, Jaroszewski L, Karlak C, Klock HE, Koesema E, Kovarik JS, Kreusch A, Kuhn P, Lesley SA, Levin I, McPhillips TM, Miller MD, Morse A, Moy K, Ouyang J, Page R, Quijano K, Robb A, Spraggon G, Stevens RC, van den Bedem H, Velasquez J, Vincent J, Wang X, West B, Wolf G, Hodgson KO, Wooley J, Wilson IA. Crystal structure of a ribose-5-phosphate isomerase RpiB (TM1080) from Thermotoga maritima at 1.90 A resolution. Proteins. 2004 Jul 1; 56(1):171-5. PMID: 15162497.
        View in: PubMed
      226. Ye Y, Godzik A. FATCAT: a web server for flexible structure comparison and structure similarity searching. Nucleic Acids Res. 2004 Jul 01; 32(Web Server issue):W582-5. PMID: 15215455; PMCID: PMC441568.
      227. Ye Y, Godzik A. Database searching by flexible protein structure alignment. Protein Sci. 2004 Jul; 13(7):1841-50. PMID: 15215527; PMCID: PMC2279924.
      228. Reed JC, Doctor KS, Godzik A. The domains of apoptosis: a genomics perspective. Sci STKE. 2004 Jun 22; 2004(239):re9. PMID: 15226512.
        View in: PubMed
      229. Schwarzenbacher R, Godzik A, Grzechnik SK, Jaroszewski L. The importance of alignment accuracy for molecular replacement. Acta Crystallogr D Biol Crystallogr. 2004 Jul; 60(Pt 7):1229-36. PMID: 15213384.
        View in: PubMed
      230. Alonso A, Burkhalter S, Sasin J, Tautz L, Bogetz J, Huynh H, Bremer MC, Holsinger LJ, Godzik A, Mustelin T. The minimal essential core of a cysteine-based protein-tyrosine phosphatase revealed by a novel 16-kDa VH1-like phosphatase, VHZ. J Biol Chem. 2004 Aug 20; 279(34):35768-74. PMID: 15201283.
        View in: PubMed
      231. Alonso A, Sasin J, Bottini N, Friedberg I, Friedberg I, Osterman A, Godzik A, Hunter T, Dixon J, Mustelin T. Protein tyrosine phosphatases in the human genome. Cell. 2004 Jun 11; 117(6):699-711. PMID: 15186772.
        View in: PubMed
      232. Friedberg I, Jaroszewski L, Ye Y, Godzik A. The interplay of fold recognition and experimental structure determination in structural genomics. Curr Opin Struct Biol. 2004 Jun; 14(3):307-12. PMID: 15193310.
        View in: PubMed
      233. Spraggon G, Schwarzenbacher R, Kreusch A, Lee CC, Abdubek P, Ambing E, Biorac T, Brinen LS, Canaves JM, Cambell J, Chiu HJ, Dai X, Deacon AM, DiDonato M, Elsliger MA, Eshagi S, Floyd R, Godzik A, Grittini C, Grzechnik SK, Hampton E, Jaroszewski L, Karlak C, Klock HE, Koesema E, Kovarik JS, Kuhn P, Levin I, McMullan D, McPhillips TM, Miller MD, Morse A, Moy K, Ouyang J, Page R, Quijano K, Robb A, Stevens RC, van den Bedem H, Velasquez J, Vincent J, von Delft F, Wang X, West B, Wolf G, Xu Q, Hodgson KO, Wooley J, Lesley SA, Wilson IA. Crystal structure of an Udp-n-acetylmuramate-alanine ligase MurC (TM0231) from Thermotoga maritima at 2.3 A resolution. Proteins. 2004 Jun 1; 55(4):1078-81. PMID: 15146505.
        View in: PubMed
      234. Schwarzenbacher R, Jaroszewski L, von Delft F, Abdubek P, Ambing E, Biorac T, Brinen LS, Canaves JM, Cambell J, Chiu HJ, Dai X, Deacon AM, DiDonato M, Elsliger MA, Eshagi S, Floyd R, Godzik A, Grittini C, Grzechnik SK, Hampton E, Karlak C, Klock HE, Koesema E, Kovarik JS, Kreusch A, Kuhn P, Lesley SA, Levin I, McMullan D, McPhillips TM, Miller MD, Morse A, Moy K, Ouyang J, Page R, Quijano K, Robb A, Spraggon G, Stevens RC, van den Bedem H, Velasquez J, Vincent J, Wang X, West B, Wolf G, Xu Q, Hodgson KO, Wooley J, Wilson IA. Crystal structure of an aspartate aminotransferase (TM1255) from Thermotoga maritima at 1.90 A resolution. Proteins. 2004 May 15; 55(3):759-63. PMID: 15103638.
        View in: PubMed
      235. Schwarzenbacher R, Jaroszewski L, von Delft F, Abdubek P, Ambing E, Biorac T, Brinen LS, Canaves JM, Cambell J, Chiu HJ, Dai X, Deacon AM, DiDonato M, Elsliger MA, Eshagi S, Floyd R, Godzik A, Grittini C, Grzechnik SK, Hampton E, Karlak C, Klock HE, Koesema E, Kovarik JS, Kreusch A, Kuhn P, Lesley SA, Levin I, McMullan D, McPhillips TM, Miller MD, Morse A, Moy K, Ouyang J, Page R, Quijano K, Robb A, Spraggon G, Stevens RC, van den Bedem H, Velasquez J, Vincent J, Wang X, West B, Wolf G, Xu Q, Hodgson KO, Wooley J, Wilson IA. Crystal structure of a type II quinolic acid phosphoribosyltransferase (TM1645) from Thermotoga maritima at 2.50 A resolution. Proteins. 2004 May 15; 55(3):768-71. PMID: 15103640.
        View in: PubMed
      236. Schwarzenbacher R, Jaroszewski L, von Delft F, Abdubek P, Ambing E, Biorac T, Brinen LS, Canaves JM, Cambell J, Chiu HJ, Dai X, Deacon AM, DiDonato M, Elsliger MA, Eshagi S, Floyd R, Godzik A, Grittini C, Grzechnik SK, Hampton E, Karlak C, Klock HE, Koesema E, Kovarik JS, Kreusch A, Kuhn P, Lesley SA, Levin I, McMullan D, McPhillips TM, Miller MD, Morse A, Moy K, Ouyang J, Page R, Quijano K, Robb A, Spraggon G, Stevens RC, van den Bedem H, Velasquez J, Vincent J, Wang X, West B, Wolf G, Xu Q, Hodgson KO, Wooley J, Wilson IA. Crystal structure of a phosphoribosylaminoimidazole mutase PurE (TM0446) from Thermotoga maritima at 1.77-A resolution. Proteins. 2004 May 1; 55(2):474-8. PMID: 15048837.
        View in: PubMed
      237. Schwarzenbacher R, Deacon AM, Jaroszewski L, Brinen LS, Canaves JM, Dai X, Elsliger MA, Floyd R, Godzik A, Grittini C, Grzechnik SK, Klock HE, Koesema E, Kovarik JS, Kreusch A, Kuhn P, Lesley SA, McMullan D, McPhillips TM, Miller MD, Morse A, Moy K, Nelson MS, Ouyang J, Page R, Robb A, Quijano K, Spraggon G, Stevens RC, van den Bedem H, Velasquez J, Vincent J, von Delft F, Wang X, West B, Wolf G, Hodgson KO, Wooley J, Wilson IA. Crystal structure of a putative glutamine amido transferase (TM1158) from Thermotoga maritima at 1.7 A resolution. Proteins. 2004 Mar 1; 54(4):801-5. PMID: 14997577.
        View in: PubMed
      238. Erlandsen H, Canaves JM, Elsliger MA, von Delft F, Brinen LS, Dai X, Deacon AM, Floyd R, Godzik A, Grittini C, Grzechnik SK, Jaroszewski L, Klock HE, Koesema E, Kovarik JS, Kreusch A, Kuhn P, Lesley SA, McMullan D, McPhillips TM, Miller MD, Morse A, Moy K, Ouyang J, Page R, Robb A, Quijano K, Schwarzenbacher R, Spraggon G, Stevens RC, van den Bedem H, Velasquez J, Vincent J, Wang X, West B, Wolf G, Hodgson KO, Wooley J, Wilson IA. Crystal structure of an HEPN domain protein (TM0613) from Thermotoga maritima at 1.75 A resolution. Proteins. 2004 Mar 1; 54(4):806-9. PMID: 14997578.
        View in: PubMed
      239. Schwarzenbacher R, von Delft F, Abdubek P, Ambing E, Biorac T, Brinen LS, Canaves JM, Cambell J, Chiu HJ, Dai X, Deacon AM, DiDonato M, Elsliger MA, Eshagi S, Floyd R, Godzik A, Grittini C, Grzechnik SK, Hampton E, Jaroszewski L, Karlak C, Klock HE, Koesema E, Kovarik JS, Kreusch A, Kuhn P, Lesley SA, Levin I, McMullan D, McPhillips TM, Miller MD, Morse A, Moy K, Ouyang J, Page R, Quijano K, Robb A, Spraggon G, Stevens RC, van den Bedem H, Velasquez J, Vincent J, Wang X, West B, Wolf G, Xu Q, Hodgson KO, Wooley J, Wilson IA. Crystal structure of a putative PII-like signaling protein (TM0021) from Thermotoga maritima at 2.5 A resolution. Proteins. 2004 Mar 1; 54(4):810-3. PMID: 14997579.
        View in: PubMed
      240. Ma H, Xiong H, Liu T, Zhang L, Godzik A, Zhang Z. Aggregate formation and synaptic abnormality induced by DSCR1. J Neurochem. 2004 Mar; 88(6):1485-96. PMID: 15009650.
        View in: PubMed
      241. Grynberg M, Godzik A. NERD: a DNA processing-related domain present in the anthrax virulence plasmid, pXO1. Trends Biochem Sci. 2004 Mar; 29(3):106-10. PMID: 15055202.
        View in: PubMed
      242. Ye Y, Godzik A. Comparative analysis of protein domain organization. Genome Res. 2004 Mar; 14(3):343-53. PMID: 14993202; PMCID: PMC535408.
      243. Sikora S, Godzik A. Combination of multiple alignment analysis and surface mapping paves a way for a detailed pathway reconstruction--the case of VHL (von Hippel-Lindau) protein and angiogenesis regulatory pathway. Protein Sci. 2004 Mar; 13(3):786-96. PMID: 14767077; PMCID: PMC2286736.
      244. Schwarzenbacher R, von Delft F, Canaves JM, Brinen LS, Dai X, Deacon AM, Elsliger MA, Eshaghi S, Floyd R, Godzik A, Grittini C, Grzechnik SK, Guda C, Jaroszewski L, Karlak C, Klock HE, Koesema E, Kovarik JS, Kreusch A, Kuhn P, Lesley SA, McMullan D, McPhillips TM, Miller MA, Miller MD, Morse A, Moy K, Ouyang J, Page R, Robb A, Rodrigues K, Selby TL, Spraggon G, Stevens RC, van den Bedem H, Velasquez J, Vincent J, Wang X, West B, Wolf G, Hodgson KO, Wooley J, Wilson IA. Crystal structure of an iron-containing 1,3-propanediol dehydrogenase (TM0920) from Thermotoga maritima at 1.3 A resolution. Proteins. 2004 Jan 1; 54(1):174-7. PMID: 14705036.
        View in: PubMed
      245. Bourne PE, Allerston CK, Krebs W, Li W, Shindyalov IN, Godzik A, Friedberg I, Liu T, Wild D, Hwang S, Ghahramani Z, Chen L, Westbrook J. The status of structural genomics defined through the analysis of current targets and structures. Pac Symp Biocomput. 2004; 375-86. PMID: 14992518.
        View in: PubMed
      246. Page R, Nelson MS, von Delft F, Elsliger MA, Canaves JM, Brinen LS, Dai X, Deacon AM, Floyd R, Godzik A, Grittini C, Grzechnik SK, Jaroszewski L, Klock HE, Koesema E, Kovarik JS, Kreusch A, Kuhn P, Lesley SA, McMullan D, McPhillips TM, Miller MD, Morse A, Moy K, Ouyang J, Robb A, Rodrigues K, Schwarzenbacher R, Spraggon G, Stevens RC, van den Bedem H, Velasquez J, Vincent J, Wang X, West B, Wolf G, Hodgson KO, Wooley J, Wilson IA. Crystal structure of gamma-glutamyl phosphate reductase (TM0293) from Thermotoga maritima at 2.0 A resolution. Proteins. 2004 Jan 1; 54(1):157-61. PMID: 14705032.
        View in: PubMed
      247. Chae HJ, Ke N, Kim HR, Chen S, Godzik A, Dickman M, Reed JC. Evolutionarily conserved cytoprotection provided by Bax Inhibitor-1 homologs from animals, plants, and yeast. Gene. 2003 Dec 24; 323:101-13. PMID: 14659883.
        View in: PubMed
      248. Huynh H, Wang X, Li W, Bottini N, Williams S, Nika K, Ishihara H, Godzik A, Mustelin T. Homotypic secretory vesicle fusion induced by the protein tyrosine phosphatase MEG2 depends on polyphosphoinositides in T cells. J Immunol. 2003 Dec 15; 171(12):6661-71. PMID: 14662869.
        View in: PubMed
      249. Bossy-Wetzel E, Barsoum MJ, Godzik A, Schwarzenbacher R, Lipton SA. Mitochondrial fission in apoptosis, neurodegeneration and aging. Curr Opin Cell Biol. 2003 Dec; 15(6):706-16. PMID: 14644195.
        View in: PubMed
      250. Zhai D, Ke N, Zhang H, Ladror U, Joseph M, Eichinger A, Godzik A, Ng SC, Reed JC. Characterization of the anti-apoptotic mechanism of Bcl-B. Biochem J. 2003 Nov 15; 376(Pt 1):229-36. PMID: 12921534; PMCID: PMC1223753.
      251. Grynberg M, Jaroszewski L, Godzik A. Domain analysis of the tubulin cofactor system: a model for tubulin folding and dimerization. BMC Bioinformatics. 2003 Oct 10; 4:46. PMID: 14536023.
        View in: PubMed
      252. Schwarzenbacher R, Canaves JM, Brinen LS, Dai X, Deacon AM, Elsliger MA, Eshaghi S, Floyd R, Godzik A, Grittini C, Grzechnik SK, Guda C, Jaroszewski L, Karlak C, Klock HE, Koesema E, Kovarik JS, Kreusch A, Kuhn P, Lesley SA, McMullan D, McPhillips TM, Miller MA, Miller MD, Morse A, Moy K, Ouyang J, Robb A, Rodrigues K, Selby TL, Spraggon G, Stevens RC, van den Bedem H, Velasquez J, Vincent J, Wang X, West B, Wolf G, Hodgson KO, Wooley J, Wilson IA. Crystal structure of uronate isomerase (TM0064) from Thermotoga maritima at 2.85 A resolution. Proteins. 2003 Oct 1; 53(1):142-5. PMID: 12945057.
        View in: PubMed
      253. Ye Y, Godzik A. Flexible structure alignment by chaining aligned fragment pairs allowing twists. Bioinformatics. 2003 Oct; 19 Suppl 2:ii246-55. PMID: 14534198.
        View in: PubMed
      254. Liu T, Rojas A, Ye Y, Godzik A. Homology modeling provides insights into the binding mode of the PAAD/DAPIN/pyrin domain, a fourth member of the CARD/DD/DED domain family. Protein Sci. 2003 Sep; 12(9):1872-81. PMID: 12930987; PMCID: PMC2323985.
      255. Stehlik C, Krajewska M, Welsh K, Krajewski S, Godzik A, Reed JC. The PAAD/PYRIN-only protein POP1/ASC2 is a modulator of ASC-mediated nuclear-factor-kappa B and pro-caspase-1 regulation. Biochem J. 2003 Jul 01; 373(Pt 1):101-13. PMID: 12656673; PMCID: PMC1223462.
      256. Doctor KS, Reed JC, Godzik A, Bourne PE. The apoptosis database. Cell Death Differ. 2003 Jun; 10(6):621-33. PMID: 12761571.
        View in: PubMed
      257. Reed JC, Doctor K, Rojas A, Zapata JM, Stehlik C, Fiorentino L, Damiano J, Roth W, Matsuzawa S, Newman R, Takayama S, Marusawa H, Xu F, Salvesen G, Godzik A. Comparative analysis of apoptosis and inflammation genes of mice and humans. Genome Res. 2003 Jun; 13(6B):1376-88. PMID: 12819136.
        View in: PubMed
      258. Stehlik C, Hayashi H, Pio F, Godzik A, Reed JC. CARD6 is a modulator of NF-kappa B activation by Nod1- and Cardiak-mediated pathways. J Biol Chem. 2003 Aug 22; 278(34):31941-9. PMID: 12775719.
        View in: PubMed
      259. Grynberg M, Erlandsen H, Godzik A. HEPN: a common domain in bacterial drug resistance and human neurodegenerative proteins. Trends Biochem Sci. 2003 May; 28(5):224-6. PMID: 12765831.
        View in: PubMed
      260. Ye Y, Jaroszewski L, Li W, Godzik A. A segment alignment approach to protein comparison. Bioinformatics. 2003 Apr 12; 19(6):742-9. PMID: 12691986.
        View in: PubMed
      261. Luz JG, Hassig CA, Pickle C, Godzik A, Meyer BJ, Wilson IA. XOL-1, primary determinant of sexual fate in C. elegans, is a GHMP kinase family member and a structural prototype for a class of developmental regulators. Genes Dev. 2003 Apr 15; 17(8):977-90. PMID: 12672694; PMCID: PMC196039.
      262. Zhao Y, Hong DH, Pawlyk B, Yue G, Adamian M, Grynberg M, Godzik A, Li T. The retinitis pigmentosa GTPase regulator (RPGR)- interacting protein: subserving RPGR function and participating in disk morphogenesis. Proc Natl Acad Sci U S A. 2003 Apr 01; 100(7):3965-70. PMID: 12651948; PMCID: PMC153031.
      263. Chen EI, Li W, Godzik A, Howard EW, Smith JW. A residue in the S2 subsite controls substrate selectivity of matrix metalloproteinase-2 and matrix metalloproteinase-9. J Biol Chem. 2003 May 09; 278(19):17158-63. PMID: 12591933.
        View in: PubMed
      264. Brinen LS, Canaves JM, Dai X, Deacon AM, Elsliger MA, Eshaghi S, Floyd R, Godzik A, Grittini C, Grzechnik SK, Guda C, Jaroszewski L, Karlak C, Klock HE, Koesema E, Kovarik JS, Kreusch A, Kuhn P, Lesley SA, McMullan D, McPhillips TM, Miller MA, Miller MD, Morse A, Moy K, Ouyang J, Robb A, Rodrigues K, Selby TL, Spraggon G, Stevens RC, van den Bedem H, Velasquez J, Vincent J, Wang X, West B, Wolf G, Taylor SS, Hodgson KO, Wooley J, Wilson IA. Crystal structure of a zinc-containing glycerol dehydrogenase (TM0423) from Thermotoga maritima at 1.5 A resolution. Proteins. 2003 Feb 1; 50(2):371-4. PMID: 12486729.
        View in: PubMed
      265. Godzik A. Fold recognition methods. Methods Biochem Anal. 2003; 44:525-46. PMID: 12647403.
        View in: PubMed
      266. Okazaki Y, Furuno M, Kasukawa T, Adachi J, Bono H, Kondo S, Nikaido I, Osato N, Saito R, Suzuki H, Yamanaka I, Kiyosawa H, Yagi K, Tomaru Y, Hasegawa Y, Nogami A, Schönbach C, Gojobori T, Baldarelli R, Hill DP, Bult C, Hume DA, Quackenbush J, Schriml LM, Kanapin A, Matsuda H, Batalov S, Beisel KW, Blake JA, Bradt D, Brusic V, Chothia C, Corbani LE, Cousins S, Dalla E, Dragani TA, Fletcher CF, Forrest A, Frazer KS, Gaasterland T, Gariboldi M, Gissi C, Godzik A, Gough J, Grimmond S, Gustincich S, Hirokawa N, Jackson IJ, Jarvis ED, Kanai A, Kawaji H, Kawasawa Y, Kedzierski RM, King BL, Konagaya A, Kurochkin IV, Lee Y, Lenhard B, Lyons PA, Maglott DR, Maltais L, Marchionni L, McKenzie L, Miki H, Nagashima T, Numata K, Okido T, Pavan WJ, Pertea G, Pesole G, Petrovsky N, Pillai R, Pontius JU, Qi D, Ramachandran S, Ravasi T, Reed JC, Reed DJ, Reid J, Ring BZ, Ringwald M, Sandelin A, Schneider C, Semple CA, Setou M, Shimada K, Sultana R, Takenaka Y, Taylor MS, Teasdale RD, Tomita M, Verardo R, Wagner L, Wahlestedt C, Wang Y, Watanabe Y, Wells C, Wilming LG, Wynshaw-Boris A, Yanagisawa M, Yang I, Yang L, Yuan Z, Zavolan M, Zhu Y, Zimmer A, Carninci P, Hayatsu N, Hirozane-Kishikawa T, Konno H, Nakamura M, Sakazume N, Sato K, Shiraki T, Waki K, Kawai J, Aizawa K, Arakawa T, Fukuda S, Hara A, Hashizume W, Imotani K, Ishii Y, Itoh M, Kagawa I, Miyazaki A, Sakai K, Sasaki D, Shibata K, Shinagawa A, Yasunishi A, Yoshino M, Waterston R, Lander ES, Rogers J, Birney E, Hayashizaki Y. Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature. 2002 Dec 05; 420(6915):563-73. PMID: 12466851.
        View in: PubMed
      267. Alonso A, Rahmouni S, Williams S, van Stipdonk M, Jaroszewski L, Godzik A, Abraham RT, Schoenberger SP, Mustelin T. Tyrosine phosphorylation of VHR phosphatase by ZAP-70. Nat Immunol. 2003 Jan; 4(1):44-8. PMID: 12447358.
        View in: PubMed
      268. Kuhn P, Lesley SA, Mathews II, Canaves JM, Brinen LS, Dai X, Deacon AM, Elsliger MA, Eshaghi S, Floyd R, Godzik A, Grittini C, Grzechnik SK, Guda C, Hodgson KO, Jaroszewski L, Karlak C, Klock HE, Koesema E, Kovarik JM, Kreusch AT, McMullan D, McPhillips TM, Miller MA, Miller M, Morse A, Moy K, Ouyang J, Robb A, Rodrigues K, Selby TL, Spraggon G, Stevens RC, Taylor SS, van den Bedem H, Velasquez J, Vincent J, Wang X, West B, Wolf G, Wooley J, Wilson IA. Crystal structure of thy1, a thymidylate synthase complementing protein from Thermotoga maritima at 2.25 A resolution. Proteins. 2002 Oct 1; 49(1):142-5. PMID: 12211025.
        View in: PubMed
      269. Lipton SA, Choi YB, Takahashi H, Zhang D, Li W, Godzik A, Bankston LA. Cysteine regulation of protein function--as exemplified by NMDA-receptor modulation. Trends Neurosci. 2002 Sep; 25(9):474-80. PMID: 12183209.
        View in: PubMed
      270. Lesley SA, Kuhn P, Godzik A, Deacon AM, Mathews I, Kreusch A, Spraggon G, Klock HE, McMullan D, Shin T, Vincent J, Robb A, Brinen LS, Miller MD, McPhillips TM, Miller MA, Scheibe D, Canaves JM, Guda C, Jaroszewski L, Selby TL, Elsliger MA, Wooley J, Taylor SS, Hodgson KO, Wilson IA, Schultz PG, Stevens RC. Structural genomics of the Thermotoga maritima proteome implemented in a high-throughput structure determination pipeline. Proc Natl Acad Sci U S A. 2002 Sep 3; 99(18):11664-9. PMID: 12193646.
        View in: PubMed
      271. Li W, Jaroszewski L, Godzik A. Sequence clustering strategies improve remote homology recognitions while reducing search times. Protein Eng. 2002 Aug; 15(8):643-9. PMID: 12364578.
        View in: PubMed
      272. Li W, Godzik A. Discovering new genes with advanced homology detection. Trends Biotechnol. 2002 Aug; 20(8):315-6. PMID: 12127268.
        View in: PubMed
      273. Fiorentino L, Stehlik C, Oliveira V, Ariza ME, Godzik A, Reed JC. A novel PAAD-containing protein that modulates NF-kappa B induction by cytokines tumor necrosis factor-alpha and interleukin-1beta. J Biol Chem. 2002 Sep 20; 277(38):35333-40. PMID: 12093792.
        View in: PubMed
      274. Jaroszewski L, Li W, Godzik A. In search for more accurate alignments in the twilight zone. Protein Sci. 2002 Jul; 11(7):1702-13. PMID: 12070323.
        View in: PubMed
      275. Wu X, Li W, Sharma V, Godzik A, Freeze HH. Cloning and characterization of glucose transporter 11, a novel sugar transporter that is alternatively spliced in various tissues. Mol Genet Metab. 2002 May; 76(1):37-45. PMID: 12175779.
        View in: PubMed
      276. Kridel SJ, Sawai H, Ratnikov BI, Chen EI, Li W, Godzik A, Strongin AY, Smith JW. A unique substrate binding mode discriminates membrane type-1 matrix metalloproteinase from other matrix metalloproteinases. J Biol Chem. 2002 Jun 28; 277(26):23788-93. PMID: 11959855.
        View in: PubMed
      277. Stenner-Liewen F, Liewen H, Zapata JM, Pawlowski K, Godzik A, Reed JC. CADD, a Chlamydia protein that interacts with death receptors. J Biol Chem. 2002 Mar 22; 277(12):9633-6. PMID: 11805081.
        View in: PubMed
      278. Li W, Jaroszewski L, Godzik A. Tolerating some redundancy significantly speeds up clustering of large protein databases. Bioinformatics. 2002 Jan; 18(1):77-82. PMID: 11836214.
        View in: PubMed
      279. Roth W, Stenner-Liewen F, Pawlowski K, Godzik A, Reed JC. Identification and characterization of DEDD2, a death effector domain-containing protein. J Biol Chem. 2002 Mar 01; 277(9):7501-8. PMID: 11741985.
        View in: PubMed
      280. Alonso A, Merlo JJ, Na S, Kholod N, Jaroszewski L, Kharitonenkov A, Williams S, Godzik A, Posada JD, Mustelin T. Inhibition of T cell antigen receptor signaling by VHR-related MKPX (VHX), a new dual specificity phosphatase related to VH1 related (VHR). J Biol Chem. 2002 Feb 15; 277(7):5524-8. PMID: 11733513.
        View in: PubMed
      281. Chen EI, Kridel SJ, Howard EW, Li W, Godzik A, Smith JW. A unique substrate recognition profile for matrix metalloproteinase-2. J Biol Chem. 2002 Feb 08; 277(6):4485-91. PMID: 11694539.
        View in: PubMed
      282. Damiano JS, Stehlik C, Pio F, Godzik A, Reed JC. CLAN, a novel human CED-4-like gene. Genomics. 2001 Jul; 75(1-3):77-83. PMID: 11472070.
        View in: PubMed
      283. Marchenko GN, Ratnikov BI, Rozanov DV, Godzik A, Deryugina EI, Strongin AY. Characterization of matrix metalloproteinase-26, a novel metalloproteinase widely expressed in cancer cells of epithelial origin. Biochem J. 2001 Jun 15; 356(Pt 3):705-18. PMID: 11389678; PMCID: PMC1221897.
      284. Pathan N, Marusawa H, Krajewska M, Matsuzawa S, Kim H, Okada K, Torii S, Kitada S, Krajewski S, Welsh K, Pio F, Godzik A, Reed JC. TUCAN, an antiapoptotic caspase-associated recruitment domain family protein overexpressed in cancer. J Biol Chem. 2001 Aug 24; 276(34):32220-9. PMID: 11408476.
        View in: PubMed
      285. Pawlowski K, Godzik A. Surface map comparison: studying function diversity of homologous proteins. J Mol Biol. 2001 Jun 08; 309(3):793-806. PMID: 11397097.
        View in: PubMed
      286. Pawlowski K, Rychlewski L, Zhang B, Godzik A. Fold predictions for bacterial genomes. J Struct Biol. 2001 May-Jun; 134(2-3):219-31. PMID: 11551181.
        View in: PubMed
      287. Li W, Jaroszewski L, Godzik A. Clustering of highly homologous sequences to reduce the size of large protein databases. Bioinformatics. 2001 Mar; 17(3):282-3. PMID: 11294794.
        View in: PubMed
      288. Zapata JM, Pawlowski K, Haas E, Ware CF, Godzik A, Reed JC. A diverse family of proteins containing tumor necrosis factor receptor-associated factor domains. J Biol Chem. 2001 Jun 29; 276(26):24242-52. PMID: 11279055.
        View in: PubMed
      289. Ke N, Godzik A, Reed JC. Bcl-B, a novel Bcl-2 family member that differentially binds and regulates Bax and Bak. J Biol Chem. 2001 Apr 20; 276(16):12481-4. PMID: 11278245.
        View in: PubMed
      290. Pawlowski K, Pio F, Chu Z, Reed JC, Godzik A. PAAD - a new protein domain associated with apoptosis, cancer and autoimmune diseases. Trends Biochem Sci. 2001 Feb; 26(2):85-7. PMID: 11166558.
        View in: PubMed
      291. Chu ZL, Pio F, Xie Z, Welsh K, Krajewska M, Krajewski S, Godzik A, Reed JC. A novel enhancer of the Apaf1 apoptosome involved in cytochrome c-dependent caspase activation and apoptosis. J Biol Chem. 2001 Mar 23; 276(12):9239-45. PMID: 11113115.
        View in: PubMed
      292. Li W, Pio F, Pawlowski K, Godzik A. Saturated BLAST: an automated multiple intermediate sequence search used to detect distant homology. Bioinformatics. 2000 Dec; 16(12):1105-10. PMID: 11159329.
        View in: PubMed
      293. Guo B, Godzik A, Reed JC. Bcl-G, a novel pro-apoptotic member of the Bcl-2 family. J Biol Chem. 2001 Jan 26; 276(4):2780-5. PMID: 11054413.
        View in: PubMed
      294. Grynberg M, Topczewski J, Godzik A, Paszewski A. The Aspergillus nidulans cysA gene encodes a novel type of serine O-acetyltransferase which is homologous to homoserine O-acetyltransferases. Microbiology. 2000 Oct; 146 ( Pt 10):2695-703. PMID: 11021945.
        View in: PubMed
      295. Zhang H, Huang Q, Ke N, Matsuyama S, Hammock B, Godzik A, Reed JC. Drosophila pro-apoptotic Bcl-2/Bax homologue reveals evolutionary conservation of cell death mechanisms. J Biol Chem. 2000 Sep 01; 275(35):27303-6. PMID: 10811653.
        View in: PubMed
      296. Jaroszewski L, Rychlewski L, Godzik A. Improving the quality of twilight-zone alignments. Protein Sci. 2000 Aug; 9(8):1487-96. PMID: 10975570.
        View in: PubMed
      297. Poole LB, Godzik A, Nayeem A, Schmitt JD. AhpF can be dissected into two functional units: tandem repeats of two thioredoxin-like folds in the N-terminus mediate electron transfer from the thioredoxin reductase-like C-terminus to AhpC. Biochemistry. 2000 Jun 06; 39(22):6602-15. PMID: 10828978.
        View in: PubMed
      298. Jaroszewski L, Rychlewski L, Reed JC, Godzik A. ATP-activated oligomerization as a mechanism for apoptosis regulation: fold and mechanism prediction for CED-4. Proteins. 2000 May 15; 39(3):197-203. PMID: 10737940.
        View in: PubMed
      299. Pawlowski K, Rychlewski L, Reed JC, Godzik A. From fold to function predictions: an apoptosis regulator protein BID. Comput Chem. 2000 May; 24(3-4):511-7. PMID: 10816020.
        View in: PubMed
      300. Zapata JM, Matsuzawa S, Godzik A, Leo E, Wasserman SA, Reed JC. The Drosophila tumor necrosis factor receptor-associated factor-1 (DTRAF1) interacts with Pelle and regulates NFkappaB activity. J Biol Chem. 2000 Apr 21; 275(16):12102-7. PMID: 10766844.
        View in: PubMed
      301. Zhang H, Xu Q, Krajewski S, Krajewska M, Xie Z, Fuess S, Kitada S, Pawlowski K, Godzik A, Reed JC. BAR: An apoptosis regulator at the intersection of caspases and Bcl-2 family proteins. Proc Natl Acad Sci U S A. 2000 Mar 14; 97(6):2597-602. PMID: 10716992; PMCID: PMC15974.
      302. Rychlewski L, Jaroszewski L, Li W, Godzik A. Comparison of sequence profiles. Strategies for structural predictions using sequence information. Protein Sci. 2000 Feb; 9(2):232-41. PMID: 10716175.
        View in: PubMed
      303. Jaroszewski L, Godzik A. Search for a new description of protein topology and local structure. Proc Int Conf Intell Syst Mol Biol. 2000; 8:211-7. PMID: 10977082.
        View in: PubMed
      304. Pawlowski K, Jaroszewski L, Rychlewski L, Godzik A. Sensitive sequence comparison as protein function predictor. Pac Symp Biocomput. 2000; 42-53. PMID: 10902155.
        View in: PubMed
      305. Schendel SL, Azimov R, Pawlowski K, Godzik A, Kagan BL, Reed JC. Ion channel activity of the BH3 only Bcl-2 family member, BID. J Biol Chem. 1999 Jul 30; 274(31):21932-6. PMID: 10419515.
        View in: PubMed
      306. Pawlowski K, Zhang B, Rychlewski L, Godzik A. The Helicobacter pylori genome: from sequence analysis to structural and functional predictions. Proteins. 1999 Jul 01; 36(1):20-30. PMID: 10373003.
        View in: PubMed
      307. Zhang B, Rychlewski L, Pawlowski K, Fetrow JS, Skolnick J, Godzik A. From fold predictions to function predictions: automation of functional site conservation analysis for functional genome predictions. Protein Sci. 1999 May; 8(5):1104-15. PMID: 10338021; PMCID: PMC2144342.
      308. Rychlewski L, Zhang B, Godzik A. Functional insights from structural predictions: analysis of the Escherichia coli genome. Protein Sci. 1999 Mar; 8(3):614-24. PMID: 10091664; PMCID: PMC2144289.
      309. Fischer D, Barret C, Bryson K, Elofsson A, Godzik A, Jones D, Karplus KJ, Kelley LA, MacCallum RM, Pawowski K, Rost B, Rychlewski L, Sternberg M. CAFASP-1: critical assessment of fully automated structure prediction methods. Proteins. 1999; Suppl 3:209-17. PMID: 10526371.
        View in: PubMed
      310. Fetrow JS, Godzik A, Skolnick J. Functional analysis of the Escherichia coli genome using the sequence-to-structure-to-function paradigm: identification of proteins exhibiting the glutaredoxin/thioredoxin disulfide oxidoreductase activity. J Mol Biol. 1998 Oct 02; 282(4):703-11. PMID: 9743619.
        View in: PubMed
      311. Jaroszewski L, Rychlewski L, Zhang B, Godzik A. Fold prediction by a hierarchy of sequence, threading, and modeling methods. Protein Sci. 1998 Jun; 7(6):1431-40. PMID: 9655348.
        View in: PubMed
      312. Fetrow JS, Godzik A. Function driven protein evolution. A possible proto-protein for the RNA-binding proteins. Pac Symp Biocomput. 1998; 485-96. PMID: 9697206.
        View in: PubMed
      313. Rychlewski L, Zhang B, Godzik A. Fold and function predictions for Mycoplasma genitalium proteins. Fold Des. 1998; 3(4):229-38. PMID: 9710568.
        View in: PubMed
      314. Zhang L, Godzik A, Skolnick J, Fetrow JS. Functional analysis of the Escherichia coli genome for members of the alpha/beta hydrolase family. Fold Des. 1998; 3(6):535-48. PMID: 9889164.
        View in: PubMed
      315. Rychlewski L, Godzik A. Secondary structure prediction using segment similarity. Protein Eng. 1997 Oct; 10(10):1143-53. PMID: 9488139.
        View in: PubMed
      316. Hu WP, Godzik A, Skolnick J. Sequence-structure specificity--how does an inverse folding approach work? Protein Eng. 1997 Apr; 10(4):317-31. PMID: 9194156.
        View in: PubMed
      317. Skolnick J, Jaroszewski L, Kolinski A, Godzik A. Derivation and testing of pair potentials for protein folding. When is the quasichemical approximation correct? Protein Sci. 1997 Mar; 6(3):676-88. PMID: 9070450.
        View in: PubMed
      318. Kolinski A, Skolnick J, Godzik A, Hu WP. A method for the prediction of surface "U"-turns and transglobular connections in small proteins. Proteins. 1997 Feb; 27(2):290-308. PMID: 9061792.
        View in: PubMed
      319. Zhang B, Jaroszewski L, Rychlewski L, Godzik A. Similarities and differences between nonhomologous proteins with similar folds: evaluation of threading strategies. Fold Des. 1997; 2(5):307-17. PMID: 9377714.
        View in: PubMed
      320. Pawlowski K, Jaroszewski L, Bierzyñski A, Godzik A. Multiple model approach--dealing with alignment ambiguities in protein modeling. Pac Symp Biocomput. 1997; 328-39. PMID: 9390303.
        View in: PubMed
      321. Godzik A. The structural alignment between two proteins: is there a unique answer? Protein Sci. 1996 Jul; 5(7):1325-38. PMID: 8819165; PMCID: PMC2143456.
      322. Pawlowski K, Bierzynski A, Godzik A. Structural diversity in a family of homologous proteins. J Mol Biol. 1996 May 03; 258(2):349-66. PMID: 8627631.
        View in: PubMed
      323. Godzik A. Knowledge-based potentials for protein folding: what can we learn from known protein structures? Structure. 1996 Apr 15; 4(4):363-6. PMID: 8740358.
        View in: PubMed
      324. Kolinski A, Skolnick J, Godzik A. An algorithm for prediction of structural elements in small proteins. Pac Symp Biocomput. 1996; 446-60. PMID: 9390250.
        View in: PubMed
      325. Godzik A, Kolinski A, Skolnick J. Are proteins ideal mixtures of amino acids? Analysis of energy parameter sets. Protein Sci. 1995 Oct; 4(10):2107-17. PMID: 8535247; PMCID: PMC2142984.
      326. Godzik A. In search of the ideal protein sequence. Protein Eng. 1995 May; 8(5):409-16. PMID: 8532661.
        View in: PubMed
      327. Godzik A, Skolnick J. Flexible algorithm for direct multiple alignment of protein structures and sequences. Comput Appl Biosci. 1994 Dec; 10(6):587-96. PMID: 7704657.
        View in: PubMed
      328. Godzik A, Skolnick J, Kolinski A. Regularities in interaction patterns of globular proteins. Protein Eng. 1993 Nov; 6(8):801-10. PMID: 8309927.
        View in: PubMed
      329. Godzik A, Kolinski A, Skolnick J. De novo and inverse folding predictions of protein structure and dynamics. J Comput Aided Mol Des. 1993 Aug; 7(4):397-438. PMID: 8229093.
        View in: PubMed
      330. Skolnick J, Kolinski A, Brooks CL, Godzik A, Rey A. A method for predicting protein structure from sequence. Curr Biol. 1993 Jul 01; 3(7):414-23. PMID: 15335708.
        View in: PubMed
      331. Skolnick J, Kolinski A, Godzik A. From independent modules to molten globules: observations on the nature of protein folding intermediates. Proc Natl Acad Sci U S A. 1993 Mar 15; 90(6):2099-100. PMID: 8460114; PMCID: PMC46030.
      332. Godzik A, Skolnick J. Sequence-structure matching in globular proteins: application to supersecondary and tertiary structure determination. Proc Natl Acad Sci U S A. 1992 Dec 15; 89(24):12098-102. PMID: 1465445; PMCID: PMC50705.
      333. Godzik A, Kolinski A, Skolnick J. Topology fingerprint approach to the inverse protein folding problem. J Mol Biol. 1992 Sep 05; 227(1):227-38. PMID: 1522587.
        View in: PubMed
      334. Godzik A, Skolnick J, Kolinski A. Simulations of the folding pathway of triose phosphate isomerase-type alpha/beta barrel proteins. Proc Natl Acad Sci U S A. 1992 Apr 01; 89(7):2629-33. PMID: 1557367; PMCID: PMC48715.
      335. Godzik A, Sander C. Conservation of residue interactions in a family of Ca-binding proteins. Protein Eng. 1989 Aug; 2(8):589-96. PMID: 2813336.
        View in: PubMed
      336. Godzik A, Boguta G, Wesolowski T. [Data bases in biochemistry--applications to analysis and prediction of protein properties and function]. Postepy Biochem. 1989; 35(1-2):45-61. PMID: 2699029.
        View in: PubMed
      337. Dadlez M, Bierzynski A, Godzik A, Sobocinska M, Kupryszewski G. Conformational role of His-12 in C-peptide of ribonuclease A. Biophys Chem. 1988 Aug; 31(1-2):175-81. PMID: 3233287.
        View in: PubMed
      338. Godzik A, Wesolowski T. On the interactions of charged side chains with the alpha-helix backbone. Biophys Chem. 1988 Aug; 31(1-2):29-34. PMID: 3233289.
        View in: PubMed
      339. Wesolowski TA, Godzik A, Geller M. Calculations of the conformational properties of acyclonucleosides. Part I. Stable conformations of acyclovir. Acta Biochim Pol. 1987; 34(2):111-22. PMID: 3673435.
        View in: PubMed
      340. Marszalek P, Godzik A. The Monte Carlo simulation of pearl chain formation. Radiat Environ Biophys. 1987; 26(4):313-7. PMID: 3685254.
        View in: PubMed
      341. Rzempoluch E, Godzik A. [Effect of human serum on the multiplication of Candida]. Med Dosw Mikrobiol. 1969; 21(2):205-9. PMID: 5356804.
        View in: PubMed