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

    Stephen Burley

    TitleAdjunct Professor
    SchoolUniversity of California, San Diego
    DepartmentSchool of Pharmacy and Pharmaceutical Science
    Address9500 Gilman Drive #0657
    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. Gathiaka S, Liu S, Chiu M, Yang H, Stuckey JA, Kang YN, Delproposto J, Kubish G, Dunbar JB, Carlson HA, Burley S, Walters WP, Amaro RE, Feher VA, Gilson MK. D3R grand challenge 2015: Evaluation of protein-ligand pose and affinity predictions. J Comput Aided Mol Des. 2016 09; 30(9):651-668. PMID: 27696240.
        View in: PubMed
      2. Adams PD, Aertgeerts K, Bauer C, Bell JA, Berman HM, Bhat TN, Blaney JM, Bolton E, Bricogne G, Brown D, Burley S, Case DA, Clark KL, Darden T, Emsley P, Feher VA, Feng Z, Groom CR, Harris SF, Hendle J, Holder T, Joachimiak A, Kleywegt GJ, Krojer T, Marcotrigiano J, Mark AE, Markley JL, Miller M, Minor W, Montelione GT, Murshudov G, Nakagawa A, Nakamura H, Nicholls A, Nicklaus M, Nolte RT, Padyana AK, Peishoff CE, Pieniazek S, Read RJ, Shao C, Sheriff S, Smart O, Soisson S, Spurlino J, Stouch T, Svobodova R, Tempel W, Terwilliger TC, Tronrud D, Velankar S, Ward SC, Warren GL, Westbrook JD, Williams P, Yang H, Young J. Outcome of the First wwPDB/CCDC/D3R Ligand Validation Workshop. Structure. 2016 Apr 05; 24(4):502-508. PMID: 27050687.
        View in: PubMed
      3. Sali A, Berman HM, Schwede T, Trewhella J, Kleywegt G, Burley S, Markley J, Nakamura H, Adams P, Bonvin AM, Chiu W, Peraro MD, Di Maio F, Ferrin TE, Grünewald K, Gutmanas A, Henderson R, Hummer G, Iwasaki K, Johnson G, Lawson CL, Meiler J, Marti-Renom MA, Montelione GT, Nilges M, Nussinov R, Patwardhan A, Rappsilber J, Read RJ, Saibil H, Schröder GF, Schwieters CD, Seidel CA, Svergun D, Topf M, Ulrich EL, Velankar S, Westbrook JD. Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop. Structure. 2015 Jul 07; 23(7):1156-67. PMID: 26095030; PMCID: PMC4933300.
      4. Goodsell DS, Dutta S, Zardecki C, Voigt M, Berman HM, Burley S. The RCSB PDB "Molecule of the Month": Inspiring a Molecular View of Biology. PLoS Biol. 2015 May; 13(5):e1002140. PMID: 25942442; PMCID: PMC4420264.
      5. Wu TJ, Wang X, Zhang Y, Meng L, Kerrigan JE, Burley S, Zheng XF. Identification of a Non-Gatekeeper Hot Spot for Drug-Resistant Mutations in mTOR Kinase. Cell Rep. 2015 Apr 21; 11(3):446-59. PMID: 25865887; PMCID: PMC4761412.
      6. Rose PW, Prlic A, Bi C, Bluhm WF, Christie CH, Dutta S, Green RK, Goodsell DS, Westbrook JD, Woo J, Young J, Zardecki C, Berman HM, Bourne PE, Burley S. The RCSB Protein Data Bank: views of structural biology for basic and applied research and education. Nucleic Acids Res. 2015 Jan; 43(Database issue):D345-56. PMID: 25428375; PMCID: PMC4383988.
      7. Berman HM, Burley S, Kleywegt GJ, Nakamura H, Markley JL. Response to On prompt update of literature references in the Protein Data Bank. Acta Crystallogr D Biol Crystallogr. 2014 Oct; 70(Pt 10):2780. PMID: 25286863; PMCID: PMC4984264.
      8. Kim SJ, Fernandez-Martinez J, Sampathkumar P, Martel A, Matsui T, Tsuruta H, Weiss TM, Shi Y, Markina-Inarrairaegui A, Bonanno JB, Sauder JM, Burley S, Chait BT, Almo SC, Rout MP, Sali A. Integrative structure-function mapping of the nucleoporin Nup133 suggests a conserved mechanism for membrane anchoring of the nuclear pore complex. Mol Cell Proteomics. 2014 Nov; 13(11):2911-26. PMID: 25139911; PMCID: PMC4223481.
      9. Korczynska M, Xiang DF, Zhang Z, Xu C, Narindoshvili T, Kamat SS, Williams HJ, Chang SS, Kolb P, Hillerich B, Sauder JM, Burley S, Almo SC, Swaminathan S, Shoichet BK, Raushel FM. Functional annotation and structural characterization of a novel lactonase hydrolyzing D-xylono-1,4-lactone-5-phosphate and L-arabino-1,4-lactone-5-phosphate. Biochemistry. 2014 Jul 22; 53(28):4727-38. PMID: 24955762; PMCID: PMC4108184.
      10. Odokonyero D, Sakai A, Patskovsky Y, Malashkevich VN, Fedorov AA, Bonanno JB, Fedorov EV, Toro R, Agarwal R, Wang C, Ozerova ND, Yew WS, Sauder JM, Swaminathan S, Burley S, Almo SC, Glasner ME. Loss of quaternary structure is associated with rapid sequence divergence in the OSBS family. Proc Natl Acad Sci U S A. 2014 Jun 10; 111(23):8535-40. PMID: 24872444; PMCID: PMC4060685.
      11. Goodsell DS, Burley S, Berman HM. Revealing structural views of biology. Biopolymers. 2013 Nov; 99(11):817-24. PMID: 23821527.
        View in: PubMed
      12. Odokonyero D, Ragumani S, Lopez MS, Bonanno JB, Ozerova ND, Woodard DR, Machala BW, Swaminathan S, Burley S, Almo SC, Glasner ME. Divergent evolution of ligand binding in the o-succinylbenzoate synthase family. Biochemistry. 2013 Oct 22; 52(42):7512-21. PMID: 24060347; PMCID: PMC3908897.
      13. Daughtry KD, Huang H, Malashkevich V, Patskovsky Y, Liu W, Ramagopal U, Sauder JM, Burley S, Almo SC, Dunaway-Mariano D, Allen KN. Structural basis for the divergence of substrate specificity and biological function within HAD phosphatases in lipopolysaccharide and sialic acid biosynthesis. Biochemistry. 2013 Aug 13; 52(32):5372-86. PMID: 23848398; PMCID: PMC3966652.
      14. Almo SC, Garforth SJ, Hillerich BS, Love JD, Seidel RD, Burley S. Protein production from the structural genomics perspective: achievements and future needs. Curr Opin Struct Biol. 2013 Jun; 23(3):335-44. PMID: 23642905; PMCID: PMC4163025.
      15. Sampathkumar P, Kim SJ, Upla P, Rice WJ, Phillips J, Timney BL, Pieper U, Bonanno JB, Fernandez-Martinez J, Hakhverdyan Z, Ketaren NE, Matsui T, Weiss TM, Stokes DL, Sauder JM, Burley S, Sali A, Rout MP, Almo SC. Structure, dynamics, evolution, and function of a major scaffold component in the nuclear pore complex. Structure. 2013 Apr 02; 21(4):560-71. PMID: 23499021; PMCID: PMC3755625.
      16. Burley S. PDB40: The Protein Data Bank celebrates its 40th birthday. Biopolymers. 2013 Mar; 99(3):165-7. PMID: 23280389.
        View in: PubMed
      17. Knapp S, Arruda P, Blagg J, Burley S, Drewry DH, Edwards A, Fabbro D, Gillespie P, Gray NS, Kuster B, Lackey KE, Mazzafera P, Tomkinson NC, Willson TM, Workman P, Zuercher WJ. A public-private partnership to unlock the untargeted kinome. Nat Chem Biol. 2013 Jan; 9(1):3-6. PMID: 23238671.
        View in: PubMed
      18. Palani K, Burley S, Swaminathan S. Structure of alanine racemase from Oenococcus oeni with bound pyridoxal 5'-phosphate. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2013 Jan 01; 69(Pt 1):15-9. PMID: 23295479; PMCID: PMC3539696.
      19. Palani K, Kumaran D, Burley S, Swaminathan S. Structure of a periplasmic glucose-binding protein from Thermotoga maritima. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2012 Dec 01; 68(Pt 12):1460-4. PMID: 23192024; PMCID: PMC3509965.
      20. Warlick BP, Evans BS, Erb TJ, Ramagopal UA, Sriram J, Imker HJ, Sauder JM, Bonanno JB, Burley S, Tabita FR, Almo SC, Sweedler JS, Gerlt JA. 1-methylthio-D-xylulose 5-phosphate methylsulfurylase: a novel route to 1-deoxy-D-xylulose 5-phosphate in Rhodospirillum rubrum. Biochemistry. 2012 Oct 23; 51(42):8324-6. PMID: 23035785; PMCID: PMC3490199.
      21. Garside EL, Schellenberg MJ, Gesner EM, Bonanno JB, Sauder JM, Burley S, Almo SC, Mehta G, MacMillan AM. Cas5d processes pre-crRNA and is a member of a larger family of CRISPR RNA endonucleases. RNA. 2012 Nov; 18(11):2020-8. PMID: 23006625; PMCID: PMC3479392.
      22. Sampathkumar P, Kim SJ, Manglicmot D, Bain KT, Gilmore J, Gheyi T, Phillips J, Pieper U, Fernandez-Martinez J, Franke JD, Matsui T, Tsuruta H, Atwell S, Thompson DA, Emtage JS, Wasserman SR, Rout MP, Sali A, Sauder JM, Almo SC, Burley S. Atomic structure of the nuclear pore complex targeting domain of a Nup116 homologue from the yeast, Candida glabrata. Proteins. 2012 Aug; 80(8):2110-6. PMID: 22544723; PMCID: PMC3686472.
      23. Wasserman SR, Koss JW, Sojitra ST, Morisco LL, Burley S. Rapid-access, high-throughput synchrotron crystallography for drug discovery. Trends Pharmacol Sci. 2012 May; 33(5):261-7. PMID: 22521107.
        View in: PubMed
      24. Hobbs ME, Malashkevich V, Williams HJ, Xu C, Sauder JM, Burley S, Almo SC, Raushel FM. Structure and catalytic mechanism of LigI: insight into the amidohydrolase enzymes of cog3618 and lignin degradation. Biochemistry. 2012 Apr 24; 51(16):3497-507. PMID: 22475079; PMCID: PMC3416963.
      25. Kamat SS, Holmes-Hampton GP, Bagaria A, Kumaran D, Tichy SE, Gheyi T, Zheng X, Bain K, Groshong C, Emtage S, Sauder JM, Burley S, Swaminathan S, Lindahl PA, Raushel FM. The catalase activity of diiron adenine deaminase. Protein Sci. 2011 Dec; 20(12):2080-94. PMID: 21998098; PMCID: PMC3302651.
      26. Agarwal R, Burley S, Swaminathan S. Structural insight into mechanism and diverse substrate selection strategy of L-ribulokinase. Proteins. 2012 Jan; 80(1):261-8. PMID: 22072612; PMCID: PMC3240725.
      27. Suttisansanee U, Lau K, Lagishetty S, Rao KN, Swaminathan S, Sauder JM, Burley S, Honek JF. Structural variation in bacterial glyoxalase I enzymes: investigation of the metalloenzyme glyoxalase I from Clostridium acetobutylicum. J Biol Chem. 2011 Nov 04; 286(44):38367-74. PMID: 21914803; PMCID: PMC3207458.
      28. Burley S, Sonenberg N. Gimme phospho-serine five! Capping enzyme guanylyltransferase recognition of the RNA polymerase II CTD. Mol Cell. 2011 Jul 22; 43(2):163-5. PMID: 21777807.
        View in: PubMed
      29. Teplova M, Malinina L, Darnell JC, Song J, Lu M, Abagyan R, Musunuru K, Teplov A, Burley S, Darnell RB, Patel DJ. Protein-RNA and protein-protein recognition by dual KH1/2 domains of the neuronal splicing factor Nova-1. Structure. 2011 Jul 13; 19(7):930-44. PMID: 21742260; PMCID: PMC3134789.
      30. Goble AM, Zhang Z, Sauder JM, Burley S, Swaminathan S, Raushel FM. Pa0148 from Pseudomonas aeruginosa catalyzes the deamination of adenine. Biochemistry. 2011 Aug 02; 50(30):6589-97. PMID: 21710971; PMCID: PMC3151671.
      31. Shi W, Punta M, Bohon J, Sauder JM, D'Mello R, Sullivan M, Toomey J, Abel D, Lippi M, Passerini A, Frasconi P, Burley S, Rost B, Chance MR. Characterization of metalloproteins by high-throughput X-ray absorption spectroscopy. Genome Res. 2011 Jun; 21(6):898-907. PMID: 21482623; PMCID: PMC3106322.
      32. Sampathkumar P, Gheyi T, Miller SA, Bain KT, Dickey M, Bonanno JB, Kim SJ, Phillips J, Pieper U, Fernandez-Martinez J, Franke JD, Martel A, Tsuruta H, Atwell S, Thompson DA, Emtage JS, Wasserman SR, Rout MP, Sali A, Sauder JM, Burley S. Structure of the C-terminal domain of Saccharomyces cerevisiae Nup133, a component of the nuclear pore complex. Proteins. 2011 May; 79(5):1672-7. PMID: 21365675; PMCID: PMC3350809.
      33. Bagaria A, Kumaran D, Burley S, Swaminathan S. Structural basis for a ribofuranosyl binding protein: insights into the furanose specific transport. Proteins. 2011 Apr; 79(4):1352-7. PMID: 21387413; PMCID: PMC3077950.
      34. Kamat SS, Bagaria A, Kumaran D, Holmes-Hampton GP, Fan H, Sali A, Sauder JM, Burley S, Lindahl PA, Swaminathan S, Raushel FM. Catalytic mechanism and three-dimensional structure of adenine deaminase. Biochemistry. 2011 Mar 22; 50(11):1917-27. PMID: 21247091; PMCID: PMC3059353.
      35. Kamat SS, Fan H, Sauder JM, Burley S, Shoichet BK, Sali A, Raushel FM. Enzymatic deamination of the epigenetic base N-6-methyladenine. J Am Chem Soc. 2011 Feb 23; 133(7):2080-3. PMID: 21275375; PMCID: PMC3043370.
      36. Zhang Z, Zhou R, Sauder JM, Tonge PJ, Burley S, Swaminathan S. Structural and functional studies of fatty acyl adenylate ligases from E. coli and L. pneumophila. J Mol Biol. 2011 Feb 18; 406(2):313-24. PMID: 21185305; PMCID: PMC3040979.
      37. Pieper U, Webb BM, Barkan DT, Schneidman-Duhovny D, Schlessinger A, Braberg H, Yang Z, Meng EC, Pettersen EF, Huang CC, Datta RS, Sampathkumar P, Madhusudhan MS, Sjölander K, Ferrin TE, Burley S, Sali A. ModBase, a database of annotated comparative protein structure models, and associated resources. Nucleic Acids Res. 2011 Jan; 39(Database issue):D465-74. PMID: 21097780; PMCID: PMC3013688.
      38. Wisedchaisri G, Dranow DM, Lie TJ, Bonanno JB, Patskovsky Y, Ozyurt SA, Sauder JM, Almo SC, Wasserman SR, Burley S, Leigh JA, Gonen T. Structural underpinnings of nitrogen regulation by the prototypical nitrogen-responsive transcriptional factor NrpR. Structure. 2010 Nov 10; 18(11):1512-21. PMID: 21070950; PMCID: PMC2996049.
      39. Sampathkumar P, Lu F, Zhao X, Li Z, Gilmore J, Bain K, Rutter ME, Gheyi T, Schwinn KD, Bonanno JB, Pieper U, Fajardo JE, Fiser A, Almo SC, Swaminathan S, Chance MR, Baker D, Atwell S, Thompson DA, Emtage JS, Wasserman SR, Sali A, Sauder JM, Burley S. Structure of a putative BenF-like porin from Pseudomonas fluorescens Pf-5 at 2.6 A resolution. Proteins. 2010 Nov 01; 78(14):3056-62. PMID: 20737437; PMCID: PMC2989796.
      40. Kikani CK, Antonysamy SA, Bonanno JB, Romero R, Zhang FF, Russell M, Gheyi T, Iizuka M, Emtage S, Sauder JM, Turk BE, Burley S, Rutter J. Structural bases of PAS domain-regulated kinase (PASK) activation in the absence of activation loop phosphorylation. J Biol Chem. 2010 Dec 24; 285(52):41034-43. PMID: 20943661; PMCID: PMC3003402.
      41. Xiang DF, Patskovsky Y, Xu C, Fedorov AA, Fedorov EV, Sisco AA, Sauder JM, Burley S, Almo SC, Raushel FM. Functional identification and structure determination of two novel prolidases from cog1228 in the amidohydrolase superfamily . Biochemistry. 2010 Aug 10; 49(31):6791-803. PMID: 20604542; PMCID: PMC2914802.
      42. Gheyi T, Rodgers L, Romero R, Sauder JM, Burley S. Mass spectrometry guided in situ proteolysis to obtain crystals for X-ray structure determination. J Am Soc Mass Spectrom. 2010 Oct; 21(10):1795-801. PMID: 20685133; PMCID: PMC2963156.
      43. Sampathkumar P, Ozyurt SA, Do J, Bain KT, Dickey M, Rodgers LA, Gheyi T, Sali A, Kim SJ, Phillips J, Pieper U, Fernandez-Martinez J, Franke JD, Martel A, Tsuruta H, Atwell S, Thompson DA, Emtage JS, Wasserman SR, Rout MP, Sauder JM, Burley S. Structures of the autoproteolytic domain from the Saccharomyces cerevisiae nuclear pore complex component, Nup145. Proteins. 2010 Jun; 78(8):1992-8. PMID: 20310066; PMCID: PMC3136511.
      44. Hall RS, Agarwal R, Hitchcock D, Sauder JM, Burley S, Swaminathan S, Raushel FM. Discovery and structure determination of the orphan enzyme isoxanthopterin deaminase . Biochemistry. 2010 May 25; 49(20):4374-82. PMID: 20415463; PMCID: PMC2892419.
      45. Hall RS, Fedorov AA, Marti-Arbona R, Fedorov EV, Kolb P, Sauder JM, Burley S, Shoichet BK, Almo SC, Raushel FM. The hunt for 8-oxoguanine deaminase. J Am Chem Soc. 2010 Feb 17; 132(6):1762-3. PMID: 20088583; PMCID: PMC2820149.
      46. Sampathkumar P, Ozyurt SA, Miller SA, Bain KT, Rutter ME, Gheyi T, Abrams B, Wang Y, Atwell S, Luz JG, Thompson DA, Wasserman SR, Emtage JS, Park EC, Rongo C, Jin Y, Klemke RL, Sauder JM, Burley S. Structures of PHR domains from Mus musculus Phr1 (Mycbp2) explain the loss-of-function mutation (Gly1092-->Glu) of the C. elegans ortholog RPM-1. J Mol Biol. 2010 Apr 09; 397(4):883-92. PMID: 20156452; PMCID: PMC2881670.
      47. Ragumani S, Sauder JM, Burley S, Swaminathan S. Structural studies on cytosolic domain of magnesium transporter MgtE from Enterococcus faecalis. Proteins. 2010 Feb 01; 78(2):487-91. PMID: 19787770; PMCID: PMC3221319.
      48. Berman HM, Kleywegt GJ, Nakamura H, Markley JL, Burley S. Safeguarding the integrity of protein archive. Nature. 2010 Jan 28; 463(7280):425. PMID: 20110969; PMCID: PMC4456675.
      49. Lakshminarasimhan D, Eswaramoorthy S, Burley S, Swaminathan S. Structure of YqgQ protein from Bacillus subtilis, a conserved hypothetical protein. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010 Jan 01; 66(Pt 1):8-11. PMID: 20057058; PMCID: PMC2805524.
      50. Rakus JF, Kalyanaraman C, Fedorov AA, Fedorov EV, Mills-Groninger FP, Toro R, Bonanno J, Bain K, Sauder JM, Burley S, Almo SC, Jacobson MP, Gerlt JA. Computation-facilitated assignment of the function in the enolase superfamily: a regiochemically distinct galactarate dehydratase from Oceanobacillus iheyensis . Biochemistry. 2009 Dec 08; 48(48):11546-58. PMID: 19883118; PMCID: PMC2787699.
      51. Buchanan SG, Hendle J, Lee PS, Smith CR, Bounaud PY, Jessen KA, Tang CM, Huser NH, Felce JD, Froning KJ, Peterman MC, Aubol BE, Gessert SF, Sauder JM, Schwinn KD, Russell M, Rooney IA, Adams J, Leon BC, Do TH, Blaney JM, Sprengeler PA, Thompson DA, Smyth L, Pelletier LA, Atwell S, Holme K, Wasserman SR, Emtage S, Burley S, Reich SH. SGX523 is an exquisitely selective, ATP-competitive inhibitor of the MET receptor tyrosine kinase with antitumor activity in vivo. Mol Cancer Ther. 2009 Dec; 8(12):3181-90. PMID: 19934279.
        View in: PubMed
      52. Sampaleanu LM, Bonanno JB, Ayers M, Koo J, Tammam S, Burley S, Almo SC, Burrows LL, Howell PL. Periplasmic domains of Pseudomonas aeruginosa PilN and PilO form a stable heterodimeric complex. J Mol Biol. 2009 Nov 20; 394(1):143-59. PMID: 19857646.
        View in: PubMed
      53. Robert F, Williams C, Yan Y, Donohue E, Cencic R, Burley S, Pelletier J. Blocking UV-induced eIF2alpha phosphorylation with small molecule inhibitors of GCN2. Chem Biol Drug Des. 2009 Jul; 74(1):57-67. PMID: 19519745.
        View in: PubMed
      54. Xiang DF, Xu C, Kumaran D, Brown AC, Sauder JM, Burley S, Swaminathan S, Raushel FM. Functional annotation of two new carboxypeptidases from the amidohydrolase superfamily of enzymes. Biochemistry. 2009 Jun 02; 48(21):4567-76. PMID: 19358546; PMCID: PMC2748308.
      55. Xiang DF, Patskovsky Y, Xu C, Meyer AJ, Sauder JM, Burley S, Almo SC, Raushel FM. Functional identification of incorrectly annotated prolidases from the amidohydrolase superfamily of enzymes. Biochemistry. 2009 May 05; 48(17):3730-42. PMID: 19281183; PMCID: PMC2683473.
      56. Leiman PG, Basler M, Ramagopal UA, Bonanno JB, Sauder JM, Pukatzki S, Burley S, Almo SC, Mekalanos JJ. Type VI secretion apparatus and phage tail-associated protein complexes share a common evolutionary origin. Proc Natl Acad Sci U S A. 2009 Mar 17; 106(11):4154-9. PMID: 19251641; PMCID: PMC2657435.
      57. Sakai A, Fedorov AA, Fedorov EV, Schnoes AM, Glasner ME, Brown S, Rutter ME, Bain K, Chang S, Gheyi T, Sauder JM, Burley S, Babbitt PC, Almo SC, Gerlt JA. Evolution of enzymatic activities in the enolase superfamily: stereochemically distinct mechanisms in two families of cis,cis-muconate lactonizing enzymes. Biochemistry. 2009 Feb 24; 48(7):1445-53. PMID: 19220063; PMCID: PMC2746992.
      58. Pieper U, Chiang R, Seffernick JJ, Brown SD, Glasner ME, Kelly L, Eswar N, Sauder JM, Bonanno JB, Swaminathan S, Burley S, Zheng X, Chance MR, Almo SC, Gerlt JA, Raushel FM, Jacobson MP, Babbitt PC, Sali A. Target selection and annotation for the structural genomics of the amidohydrolase and enolase superfamilies. J Struct Funct Genomics. 2009 Apr; 10(2):107-25. PMID: 19219566; PMCID: PMC2693957.
      59. Schwede T, Sali A, Honig B, Levitt M, Berman HM, Jones D, Brenner SE, Burley S, 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; PMCID: PMC2739730.
      60. Rao KN, Burley S, Swaminathan S. UPF201 archaeal specific family members reveal structural similarity to RNA-binding proteins but low likelihood for RNA-binding function. PLoS One. 2008; 3(12):e3903. PMID: 19079550; PMCID: PMC2596488.
      61. Ragumani S, Kumaran D, Burley S, Swaminathan S. Crystal structure of a putative lysostaphin peptidase from Vibrio cholerae. Proteins. 2008 Aug 15; 72(3):1096-103. PMID: 18498110; PMCID: PMC3614409.
      62. Madegowda M, Eswaramoorthy S, Burley S, Swaminathan S. X-ray crystal structure of the B component of Hemolysin BL from Bacillus cereus. Proteins. 2008 May 01; 71(2):534-40. PMID: 18175317; PMCID: PMC3220058.
      63. Agarwal R, Burley S, Swaminathan S. A novel mode of dimerization via formation of a glutamate anhydride crosslink in a protein crystal structure. Proteins. 2008 May 01; 71(2):1038-41. PMID: 18247349.
        View in: PubMed
      64. Tyagi R, Eswaramoorthy S, Burley S, Raushel FM, Swaminathan S. A common catalytic mechanism for proteins of the HutI family. Biochemistry. 2008 May 20; 47(20):5608-15. PMID: 18442260; PMCID: PMC3232013.
      65. O'Hare T, Eide CA, Tyner JW, Corbin AS, Wong MJ, Buchanan S, Holme K, Jessen KA, Tang C, Lewis HA, Romero RD, Burley S, Deininger MW. SGX393 inhibits the CML mutant Bcr-AblT315I and preempts in vitro resistance when combined with nilotinib or dasatinib. Proc Natl Acad Sci U S A. 2008 Apr 08; 105(14):5507-12. PMID: 18367669; PMCID: PMC2291110.
      66. Rao KN, Burley S, Swaminathan S. Crystal structure of a conserved protein of unknown function (MJ1651) from Methanococcus jannaschii. Proteins. 2008 Feb 01; 70(2):572-7. PMID: 17910070.
        View in: PubMed
      67. Gräslund S, Nordlund P, Weigelt J, Hallberg BM, Bray J, Gileadi O, Knapp S, Oppermann U, Arrowsmith C, Hui R, Ming J, dhe-Paganon S, Park HW, Savchenko A, Yee A, Edwards A, Vincentelli R, Cambillau C, Kim R, Kim SH, Rao Z, Shi Y, Terwilliger TC, Kim CY, Hung LW, Waldo GS, Peleg Y, Albeck S, Unger T, Dym O, Prilusky J, Sussman JL, Stevens RC, Lesley SA, Wilson IA, Joachimiak A, Collart F, Dementieva I, Donnelly MI, Eschenfeldt WH, Kim Y, Stols L, Wu R, Zhou M, Burley S, Emtage JS, Sauder JM, Thompson D, Bain K, Luz J, Gheyi T, Zhang F, Atwell S, Almo SC, Bonanno JB, Fiser A, Swaminathan S, Studier FW, Chance MR, Sali A, Acton TB, Xiao R, Zhao L, Ma LC, Hunt JF, Tong L, Cunningham K, Inouye M, Anderson S, Janjua H, Shastry R, Ho CK, Wang D, Wang H, Jiang M, Montelione GT, Stuart DI, Owens RJ, Daenke S, Schütz A, Heinemann U, Yokoyama S, Büssow K, Gunsalus KC. Protein production and purification. Nat Methods. 2008 Feb; 5(2):135-46. PMID: 18235434; PMCID: PMC3178102.
      68. Agarwal R, Burley S, Swaminathan S. Structure of human dual specificity protein phosphatase 23, VHZ, enzyme-substrate/product complex. J Biol Chem. 2008 Apr 04; 283(14):8946-53. PMID: 18245086.
        View in: PubMed
      69. Burley S, Joachimiak A, Montelione GT, Wilson IA. Contributions to the NIH-NIGMS Protein Structure Initiative from the PSI Production Centers. Structure. 2008 Jan; 16(1):5-11. PMID: 18184575; PMCID: PMC2678832.
      70. Sauder MJ, Rutter ME, Bain K, Rooney I, Gheyi T, Atwell S, Thompson DA, Emtage S, Burley S. High throughput protein production and crystallization at NYSGXRC. Methods Mol Biol. 2008; 426:561-75. PMID: 18542890.
        View in: PubMed
      71. Almo SC, Bonanno JB, Sauder JM, Emtage S, Dilorenzo TP, Malashkevich V, Wasserman SR, Swaminathan S, Eswaramoorthy S, Agarwal R, Kumaran D, Madegowda M, Ragumani S, Patskovsky Y, Alvarado J, Ramagopal UA, Faber-Barata J, Chance MR, Sali A, Fiser A, Zhang ZY, Lawrence DS, Burley S. Structural genomics of protein phosphatases. J Struct Funct Genomics. 2007 Sep; 8(2-3):121-40. PMID: 18058037; PMCID: PMC4163028.
      72. Tyagi R, Kumaran D, Burley S, Swaminathan S. X-ray structure of imidazolonepropionase from Agrobacterium tumefaciens at 1.87 A resolution. Proteins. 2007 Nov 15; 69(3):652-8. PMID: 17640072.
        View in: PubMed
      73. Tyagi R, Burley S, Swaminathan S. X-ray structures of two proteins belonging to Pfam DUF178 revealed unexpected structural similarity to the DUF191 Pfam family. BMC Struct Biol. 2007 Oct 01; 7:62. PMID: 17908300; PMCID: PMC2174479.
      74. Agarwal R, Burley S, Swaminathan S. Structural analysis of a ternary complex of allantoate amidohydrolase from Escherichia coli reveals its mechanics. J Mol Biol. 2007 Apr 27; 368(2):450-63. PMID: 17362992.
        View in: PubMed
      75. Sabini E, Hazra S, Konrad M, Burley S, Lavie A. Structural basis for activation of the therapeutic L-nucleoside analogs 3TC and troxacitabine by human deoxycytidine kinase. Nucleic Acids Res. 2007; 35(1):186-92. PMID: 17158155; PMCID: PMC1802566.
      76. Rao KN, Bonanno JB, Burley S, Swaminathan S. Crystal structure of glycerophosphodiester phosphodiesterase from Agrobacterium tumefaciens by SAD with a large asymmetric unit. Proteins. 2006 Nov 01; 65(2):514-8. PMID: 16909422.
        View in: PubMed
      77. Kumaran D, Bonanno JB, Burley S, Swaminathan S. Crystal structure of phosphatidylglycerophosphatase (PGPase), a putative membrane-bound lipid phosphatase, reveals a novel binuclear metal binding site and two "proton wires". Proteins. 2006 Sep 01; 64(4):851-62. PMID: 16838328.
        View in: PubMed
      78. Rao KN, Kumaran D, Seetharaman J, Bonanno JB, Burley S, Swaminathan S. Crystal structure of trehalose-6-phosphate phosphatase-related protein: biochemical and biological implications. Protein Sci. 2006 Jul; 15(7):1735-44. PMID: 16815921; PMCID: PMC2242562.
      79. Eswaramoorthy S, Bonanno JB, Burley S, Swaminathan S. Mechanism of action of a flavin-containing monooxygenase. Proc Natl Acad Sci U S A. 2006 Jun 27; 103(26):9832-7. PMID: 16777962; PMCID: PMC1502539.
      80. Seetharaman J, Rajashankar KR, Solorzano V, Kniewel R, Lima CD, Bonanno JB, Burley S, Swaminathan S. Crystal structures of two putative phosphoheptose isomerases. Proteins. 2006 Jun 01; 63(4):1092-6. PMID: 16477602; PMCID: PMC1769519.
      81. Seetharaman J, Kumaran D, Bonanno JB, Burley S, Swaminathan S. Crystal structure of a putative HTH-type transcriptional regulator yxaF from Bacillus subtilis. Proteins. 2006 Jun 01; 63(4):1087-91. PMID: 16475182; PMCID: PMC1752215.
      82. Bellsolell L, Cho-Park PF, Poulin F, Sonenberg N, Burley S. Two structurally atypical HEAT domains in the C-terminal portion of human eIF4G support binding to eIF4A and Mnk1. Structure. 2006 May; 14(5):913-23. PMID: 16698552.
        View in: PubMed
      83. Burley S. Cancer and kinases: reports from the front line. Genome Biol. 2006; 7(4):314. PMID: 16677415; PMCID: PMC1557988.
      84. Agarwal R, Bonanno JB, Burley S, Swaminathan S. Structure determination of an FMN reductase from Pseudomonas aeruginosa PA01 using sulfur anomalous signal. Acta Crystallogr D Biol Crystallogr. 2006 Apr; 62(Pt 4):383-91. PMID: 16552139; PMCID: PMC1431508.
      85. Nair SK, Burley S. Structural aspects of interactions within the Myc/Max/Mad network. Curr Top Microbiol Immunol. 2006; 302:123-43. PMID: 16620027.
        View in: PubMed
      86. Badger J, Hendle J, Burley S, Kissinger CR. Deposit3D: a tool for automating structure depositions to the Protein Data Bank. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2005 Sep 01; 61(Pt 9):818-20. PMID: 16511167; PMCID: PMC1978113.
      87. Burley S, Park F. Meeting the challenges of drug discovery: a multidisciplinary re-evaluation of current practices. Keystone Symposium 'Meeting the Challenges of Drug Discovery', Vancouver, Canada, 15-19 January 2005. Genome Biol. 2005; 6(7):330. PMID: 15998459; PMCID: PMC1175982.
      88. Padyana AK, Qiu H, Roll-Mecak A, Hinnebusch AG, Burley S. Structural basis for autoinhibition and mutational activation of eukaryotic initiation factor 2alpha protein kinase GCN2. J Biol Chem. 2005 Aug 12; 280(32):29289-99. PMID: 15964839.
        View in: PubMed
      89. Matte A, Louie GV, Sivaraman J, Cygler M, Burley S. Structure of the pseudouridine synthase RsuA from Haemophilus influenzae. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2005 Apr 01; 61(Pt 4):350-4. PMID: 16511038; PMCID: PMC1952432.
      90. Gao X, Bain K, Bonanno JB, Buchanan M, Henderson D, Lorimer D, Marsh C, Reynes JA, Sauder JM, Schwinn K, Thai C, Burley S. High-throughput limited proteolysis/mass spectrometry for protein domain elucidation. J Struct Funct Genomics. 2005; 6(2-3):129-34. PMID: 16211509.
        View in: PubMed
      91. Bonanno JB, Almo SC, Bresnick A, Chance MR, Fiser A, Swaminathan S, Jiang J, Studier FW, Shapiro L, Lima CD, Gaasterland TM, Sali A, Bain K, Feil I, Gao X, Lorimer D, Ramos A, Sauder JM, Wasserman SR, Emtage S, D'Amico KL, Burley S. New York-Structural GenomiX Research Consortium (NYSGXRC): a large scale center for the protein structure initiative. J Struct Funct Genomics. 2005; 6(2-3):225-32. PMID: 16211523.
        View in: PubMed
      92. Sickmier EA, Brekasis D, Paranawithana S, Bonanno JB, Paget MS, Burley S, Kielkopf CL. X-ray structure of a Rex-family repressor/NADH complex insights into the mechanism of redox sensing. Structure. 2005 Jan; 13(1):43-54. PMID: 15642260.
        View in: PubMed
      93. Niessing D, Hüttelmaier S, Zenklusen D, Singer RH, Burley S. She2p is a novel RNA binding protein with a basic helical hairpin motif. Cell. 2004 Nov 12; 119(4):491-502. PMID: 15537539.
        View in: PubMed
      94. Atwell S, Adams JM, Badger J, Buchanan MD, Feil IK, Froning KJ, Gao X, Hendle J, Keegan K, Leon BC, Müller-Dieckmann HJ, Nienaber VL, Noland BW, Post K, Rajashankar KR, Ramos A, Russell M, Burley S, Buchanan SG. A novel mode of Gleevec binding is revealed by the structure of spleen tyrosine kinase. J Biol Chem. 2004 Dec 31; 279(53):55827-32. PMID: 15507431.
        View in: PubMed
      95. Roll-Mecak A, Alone P, Cao C, Dever TE, Burley S. X-ray structure of translation initiation factor eIF2gamma: implications for tRNA and eIF2alpha binding. J Biol Chem. 2004 Mar 12; 279(11):10634-42. PMID: 14688270.
        View in: PubMed
      96. Lewis HA, Buchanan SG, Burley S, Conners K, Dickey M, Dorwart M, Fowler R, Gao X, Guggino WB, Hendrickson WA, Hunt JF, Kearins MC, Lorimer D, Maloney PC, Post KW, Rajashankar KR, Rutter ME, Sauder JM, Shriver S, Thibodeau PH, Thomas PJ, Zhang M, Zhao X, Emtage S. Structure of nucleotide-binding domain 1 of the cystic fibrosis transmembrane conductance regulator. EMBO J. 2004 Jan 28; 23(2):282-93. PMID: 14685259; PMCID: PMC1271750.
      97. Deo RC, Schmidt EF, Elhabazi A, Togashi H, Burley S, Strittmatter SM. Structural bases for CRMP function in plexin-dependent semaphorin3A signaling. EMBO J. 2004 Jan 14; 23(1):9-22. PMID: 14685275; PMCID: PMC1271659.
      98. Padyana AK, Burley S. Crystal structure of shikimate 5-dehydrogenase (SDH) bound to NADP: insights into function and evolution. Structure. 2003 Aug; 11(8):1005-13. PMID: 12906831.
        View in: PubMed
      99. Kamada K, Hanaoka F, Burley S. Crystal structure of the MazE/MazF complex: molecular bases of antidote-toxin recognition. Mol Cell. 2003 Apr; 11(4):875-84. PMID: 12718874.
        View in: PubMed
      100. Trester-Zedlitz M, Kamada K, Burley S, Fenyö D, Chait BT, Muir TW. A modular cross-linking approach for exploring protein interactions. J Am Chem Soc. 2003 Mar 05; 125(9):2416-25. PMID: 12603129.
        View in: PubMed
      101. Kamada K, Roeder RG, Burley S. Molecular mechanism of recruitment of TFIIF- associating RNA polymerase C-terminal domain phosphatase (FCP1) by transcription factor IIF. Proc Natl Acad Sci U S A. 2003 Mar 04; 100(5):2296-9. PMID: 12591941; PMCID: PMC151334.
      102. Nair SK, Burley S. X-ray structures of Myc-Max and Mad-Max recognizing DNA. Molecular bases of regulation by proto-oncogenic transcription factors. Cell. 2003 Jan 24; 112(2):193-205. PMID: 12553908.
        View in: PubMed
      103. Ray SS, Bonanno JB, Chen H, de Lencastre H, Wu S, Tomasz A, Burley S. X-ray structure of an M. jannaschii DNA-binding protein: implications for antibiotic resistance in S. aureus. Proteins. 2003 Jan 01; 50(1):170-3. PMID: 12471609.
        View in: PubMed
      104. Burley S, Bonanno JB. Structural genomics. Methods Biochem Anal. 2003; 44:591-612. PMID: 12647406.
        View in: PubMed
      105. Zuberek J, Wyslouch-Cieszynska A, Niedzwiecka A, Dadlez M, Stepinski J, Augustyniak W, Gingras AC, Zhang Z, Burley S, Sonenberg N, Stolarski R, Darzynkiewicz E. Phosphorylation of eIF4E attenuates its interaction with mRNA 5' cap analogs by electrostatic repulsion: intein-mediated protein ligation strategy to obtain phosphorylated protein. RNA. 2003 Jan; 9(1):52-61. PMID: 12554876; PMCID: PMC1370370.
      106. Shin BS, Maag D, Roll-Mecak A, Arefin MS, Burley S, Lorsch JR, Dever TE. Uncoupling of initiation factor eIF5B/IF2 GTPase and translational activities by mutations that lower ribosome affinity. Cell. 2002 Dec 27; 111(7):1015-25. PMID: 12507428.
        View in: PubMed
      107. Pilloff D, Dabovic K, Romanowski MJ, Bonanno JB, Doherty M, Burley S, Leyh TS. The kinetic mechanism of phosphomevalonate kinase. J Biol Chem. 2003 Feb 14; 278(7):4510-5. PMID: 12424232.
        View in: PubMed
      108. Ray SS, Bonanno JB, Rajashankar KR, Pinho MG, He G, De Lencastre H, Tomasz A, Burley S. Cocrystal structures of diaminopimelate decarboxylase: mechanism, evolution, and inhibition of an antibiotic resistance accessory factor. Structure. 2002 Nov; 10(11):1499-508. PMID: 12429091.
        View in: PubMed
      109. Kielkopf CL, Burley S. X-ray structures of threonine aldolase complexes: structural basis of substrate recognition. Biochemistry. 2002 Oct 01; 41(39):11711-20. PMID: 12269813.
        View in: PubMed
      110. Deaconescu AM, Roll-Mecak A, Bonanno JB, Gerchman SE, Kycia H, Studier FW, Burley S. X-ray structure of Saccharomyces cerevisiae homologous mitochondrial matrix factor 1 (Hmf1). Proteins. 2002 Aug 01; 48(2):431-6. PMID: 12112709.
        View in: PubMed
      111. Niedzwiecka A, Marcotrigiano J, Stepinski J, Jankowska-Anyszka M, Wyslouch-Cieszynska A, Dadlez M, Gingras AC, Mak P, Darzynkiewicz E, Sonenberg N, Burley S, Stolarski R. Biophysical studies of eIF4E cap-binding protein: recognition of mRNA 5' cap structure and synthetic fragments of eIF4G and 4E-BP1 proteins. J Mol Biol. 2002 Jun 07; 319(3):615-35. PMID: 12054859.
        View in: PubMed
      112. Burley S, Bonanno JB. Structural genomics of proteins from conserved biochemical pathways and processes. Curr Opin Struct Biol. 2002 Jun; 12(3):383-91. PMID: 12127459.
        View in: PubMed
      113. Romanowski MJ, Burley S. Crystal structure of the Escherichia coli shikimate kinase I (AroK) that confers sensitivity to mecillinam. Proteins. 2002 Jun 01; 47(4):558-62. PMID: 12001235.
        View in: PubMed
      114. Groft CM, Burley S. Recognition of eIF4G by rotavirus NSP3 reveals a basis for mRNA circularization. Mol Cell. 2002 Jun; 9(6):1273-83. PMID: 12086624.
        View in: PubMed
      115. Romanowski MJ, Bonanno JB, Burley S. Crystal structure of the Escherichia coli glucose-inhibited division protein B (GidB) reveals a methyltransferase fold. Proteins. 2002 Jun 01; 47(4):563-7. PMID: 12001236.
        View in: PubMed
      116. Romanowski MJ, Bonanno JB, Burley S. Crystal structure of the Streptococcus pneumoniae phosphomevalonate kinase, a member of the GHMP kinase superfamily. Proteins. 2002 Jun 01; 47(4):568-71. PMID: 12001237.
        View in: PubMed
      117. Romanowski MJ, Gibney SA, Burley S. Crystal structure of the Escherichia coli SbmC protein that protects cells from the DNA replication inhibitor microcin B17. Proteins. 2002 May 15; 47(3):403-7. PMID: 11948793.
        View in: PubMed
      118. Soccio RE, Adams RM, Romanowski MJ, Sehayek E, Burley S, Breslow JL. The cholesterol-regulated StarD4 gene encodes a StAR-related lipid transfer protein with two closely related homologues, StarD5 and StarD6. Proc Natl Acad Sci U S A. 2002 May 14; 99(10):6943-8. PMID: 12011452; PMCID: PMC124508.
      119. Romanowski MJ, Soccio RE, Breslow JL, Burley S. Crystal structure of the Mus musculus cholesterol-regulated START protein 4 (StarD4) containing a StAR-related lipid transfer domain. Proc Natl Acad Sci U S A. 2002 May 14; 99(10):6949-54. PMID: 12011453; PMCID: PMC124509.
      120. Burley S, Bonanno JB. Structuring the universe of proteins. Annu Rev Genomics Hum Genet. 2002; 3:243-62. PMID: 12194989.
        View in: PubMed
      121. Chance MR, Bresnick AR, Burley S, Jiang JS, Lima CD, Sali A, Almo SC, Bonanno JB, Buglino JA, Boulton S, Chen H, Eswar N, He G, Huang R, Ilyin V, McMahan L, Pieper U, Ray S, Vidal M, Wang LK. Structural genomics: a pipeline for providing structures for the biologist. Protein Sci. 2002 Apr; 11(4):723-38. PMID: 11910018; PMCID: PMC2373525.
      122. Burley S, Kamada K. Transcription factor complexes. Curr Opin Struct Biol. 2002 Apr; 12(2):225-30. PMID: 11959501.
        View in: PubMed
      123. Wolf E, De Angelis J, Khalil EM, Cole PA, Burley S. X-ray crystallographic studies of serotonin N-acetyltransferase catalysis and inhibition. J Mol Biol. 2002 Mar 22; 317(2):215-24. PMID: 11902838.
        View in: PubMed
      124. Scheibner KA, De Angelis J, Burley S, Cole PA. Investigation of the roles of catalytic residues in serotonin N-acetyltransferase. J Biol Chem. 2002 May 17; 277(20):18118-26. PMID: 11884405.
        View in: PubMed
      125. Deo RC, Groft CM, Rajashankar KR, Burley S. Recognition of the rotavirus mRNA 3' consensus by an asymmetric NSP3 homodimer. Cell. 2002 Jan 11; 108(1):71-81. PMID: 11792322.
        View in: PubMed
      126. Marcotrigiano J, Burley S. Structural biology of eIF4F: mRNA recognition and preparation in eukaryotic translation initiation. Adv Protein Chem. 2002; 61:269-97. PMID: 12461826.
        View in: PubMed
      127. Roll-Mecak A, Shin BS, Dever TE, Burley S. Engaging the ribosome: universal IFs of translation. Trends Biochem Sci. 2001 Dec; 26(12):705-9. PMID: 11738593.
        View in: PubMed
      128. Bonanno JB, Edo C, Eswar N, Pieper U, Romanowski MJ, Ilyin V, Gerchman SE, Kycia H, Studier FW, Sali A, Burley S. Structural genomics of enzymes involved in sterol/isoprenoid biosynthesis. Proc Natl Acad Sci U S A. 2001 Nov 06; 98(23):12896-901. PMID: 11698677; PMCID: PMC60796.
      129. Gingras AC, Raught B, Gygi SP, Niedzwiecka A, Miron M, Burley S, Polakiewicz RD, Wyslouch-Cieszynska A, Aebersold R, Sonenberg N. Hierarchical phosphorylation of the translation inhibitor 4E-BP1. Genes Dev. 2001 Nov 01; 15(21):2852-64. PMID: 11691836; PMCID: PMC312813.
      130. Olson WK, Bansal M, Burley S, Dickerson RE, Gerstein M, Harvey SC, Heinemann U, Lu XJ, Neidle S, Shakked Z, Sklenar H, Suzuki M, Tung CS, Westhof E, Wolberger C, Berman HM. A standard reference frame for the description of nucleic acid base-pair geometry. J Mol Biol. 2001 Oct 12; 313(1):229-37. PMID: 11601858.
        View in: PubMed
      131. Kielkopf CL, Rodionova NA, Green MR, Burley S. A novel peptide recognition mode revealed by the X-ray structure of a core U2AF35/U2AF65 heterodimer. Cell. 2001 Sep 07; 106(5):595-605. PMID: 11551507.
        View in: PubMed
      132. Kamada K, Shu F, Chen H, Malik S, Stelzer G, Roeder RG, Meisterernst M, Burley S. Crystal structure of negative cofactor 2 recognizing the TBP-DNA transcription complex. Cell. 2001 Jul 13; 106(1):71-81. PMID: 11461703.
        View in: PubMed
      133. Deo RC, Sonenberg N, Burley S. X-ray structure of the human hyperplastic discs protein: an ortholog of the C-terminal domain of poly(A)-binding protein. Proc Natl Acad Sci U S A. 2001 Apr 10; 98(8):4414-9. PMID: 11287654; PMCID: PMC31849.
      134. Kamada K, De Angelis J, Roeder RG, Burley S. Crystal structure of the C-terminal domain of the RAP74 subunit of human transcription factor IIF. Proc Natl Acad Sci U S A. 2001 Mar 13; 98(6):3115-20. PMID: 11248041; PMCID: PMC30616.
      135. Houbaviy HB, Burley S. Thermodynamic analysis of the interaction between YY1 and the AAV P5 promoter initiator element. Chem Biol. 2001 Feb; 8(2):179-87. PMID: 11251291.
        View in: PubMed
      136. Marcotrigiano J, Lomakin IB, Sonenberg N, Pestova TV, Hellen CU, Burley S. A conserved HEAT domain within eIF4G directs assembly of the translation initiation machinery. Mol Cell. 2001 Jan; 7(1):193-203. PMID: 11172724.
        View in: PubMed
      137. Khaleghpour K, Svitkin YV, Craig AW, DeMaria CT, Deo RC, Burley S, Sonenberg N. Translational repression by a novel partner of human poly(A) binding protein, Paip2. Mol Cell. 2001 Jan; 7(1):205-16. PMID: 11172725.
        View in: PubMed
      138. Dever TE, Roll-Mecak A, Choi SK, Lee JH, Cao C, Shin BS, Burley S. Universal translation initiation factor IF2/eIF5B. Cold Spring Harb Symp Quant Biol. 2001; 66:417-24. PMID: 12762044.
        View in: PubMed
      139. Groft CM, Beckmann R, Sali A, Burley S. Crystal structures of ribosome anti-association factor IF6. Nat Struct Biol. 2000 Dec; 7(12):1156-64. PMID: 11101899.
        View in: PubMed
      140. Roll-Mecak A, Cao C, Dever TE, Burley S. X-Ray structures of the universal translation initiation factor IF2/eIF5B: conformational changes on GDP and GTP binding. Cell. 2000 Nov 22; 103(5):781-92. PMID: 11114334.
        View in: PubMed
      141. Burley S. An overview of structural genomics. Nat Struct Biol. 2000 Nov; 7 Suppl:932-4. PMID: 11103991.
        View in: PubMed
      142. Choi SK, Olsen DS, Roll-Mecak A, Martung A, Remo KL, Burley S, Hinnebusch AG, Dever TE. Physical and functional interaction between the eukaryotic orthologs of prokaryotic translation initiation factors IF1 and IF2. Mol Cell Biol. 2000 Oct; 20(19):7183-91. PMID: 10982835; PMCID: PMC86272.
      143. Jensen KB, Musunuru K, Lewis HA, Burley S, Darnell RB. The tetranucleotide UCAY directs the specific recognition of RNA by the Nova K-homology 3 domain. Proc Natl Acad Sci U S A. 2000 May 23; 97(11):5740-5. PMID: 10811881; PMCID: PMC18503.
      144. Nair SK, Burley S. Recognizing DNA in the library. Nature. 2000 Apr 13; 404(6779):715, 717-8. PMID: 10783871.
        View in: PubMed
      145. Gajiwala KS, Chen H, Cornille F, Roques BP, Reith W, Mach B, Burley S. Structure of the winged-helix protein hRFX1 reveals a new mode of DNA binding. Nature. 2000 Feb 24; 403(6772):916-21. PMID: 10706293.
        View in: PubMed
      146. Lewis HA, Musunuru K, Jensen KB, Edo C, Chen H, Darnell RB, Burley S. Sequence-specific RNA binding by a Nova KH domain: implications for paraneoplastic disease and the fragile X syndrome. Cell. 2000 Feb 04; 100(3):323-32. PMID: 10676814.
        View in: PubMed
      147. Rhodes D, Burley S. Protein-nucleic acid interactions. Curr Opin Struct Biol. 2000 Feb; 10(1):75-7. PMID: 10766517.
        View in: PubMed
      148. Gajiwala KS, Burley S. Winged helix proteins. Curr Opin Struct Biol. 2000 Feb; 10(1):110-6. PMID: 10679470.
        View in: PubMed
      149. Gajiwala KS, Burley S. HDEA, a periplasmic protein that supports acid resistance in pathogenic enteric bacteria. J Mol Biol. 2000 Jan 21; 295(3):605-12. PMID: 10623550.
        View in: PubMed
      150. Patikoglou GA, Kim JL, Sun L, Yang SH, Kodadek T, Burley S. TATA element recognition by the TATA box-binding protein has been conserved throughout evolution. Genes Dev. 1999 Dec 15; 13(24):3217-30. PMID: 10617571; PMCID: PMC317201.
      151. Burley S, Almo SC, Bonanno JB, Capel M, Chance MR, Gaasterland T, Lin D, Sali A, Studier FW, Swaminathan S. Structural genomics: beyond the human genome project. Nat Genet. 1999 Oct; 23(2):151-7. PMID: 10508510.
        View in: PubMed
      152. Deo RC, Bonanno JB, Sonenberg N, Burley S. Recognition of polyadenylate RNA by the poly(A)-binding protein. Cell. 1999 Sep 17; 98(6):835-45. PMID: 10499800.
        View in: PubMed
      153. Marcotrigiano J, Gingras AC, Sonenberg N, Burley S. Cap-dependent translation initiation in eukaryotes is regulated by a molecular mimic of eIF4G. Mol Cell. 1999 Jun; 3(6):707-16. PMID: 10394359.
        View in: PubMed
      154. Lee JH, Choi SK, Roll-Mecak A, Burley S, Dever TE. Universal conservation in translation initiation revealed by human and archaeal homologs of bacterial translation initiation factor IF2. Proc Natl Acad Sci U S A. 1999 Apr 13; 96(8):4342-7. PMID: 10200264; PMCID: PMC16334.
      155. Lewis HA, Chen H, Edo C, Buckanovich RJ, Yang YY, Musunuru K, Zhong R, Darnell RB, Burley S. Crystal structures of Nova-1 and Nova-2 K-homology RNA-binding domains. Structure. 1999 Feb 15; 7(2):191-203. PMID: 10368286.
        View in: PubMed
      156. Burley S, Roeder RG. TATA box mimicry by TFIID: autoinhibition of pol II transcription. Cell. 1998 Sep 04; 94(5):551-3. PMID: 9741619.
        View in: PubMed
      157. Wolf E, Vassilev A, Makino Y, Sali A, Nakatani Y, Burley S. Crystal structure of a GCN5-related N-acetyltransferase: Serratia marcescens aminoglycoside 3-N-acetyltransferase. Cell. 1998 Aug 21; 94(4):439-49. PMID: 9727487.
        View in: PubMed
      158. Sturm NS, Lin Y, Burley S, Krstenansky JL, Ahn JM, Azizeh BY, Trivedi D, Hruby VJ. Structure-function studies on positions 17, 18, and 21 replacement analogues of glucagon: the importance of charged residues and salt bridges in glucagon biological activity. J Med Chem. 1998 Jul 16; 41(15):2693-700. PMID: 9667960.
        View in: PubMed
      159. Rom E, Kim HC, Gingras AC, Marcotrigiano J, Favre D, Olsen H, Burley S, Sonenberg N. Cloning and characterization of 4EHP, a novel mammalian eIF4E-related cap-binding protein. J Biol Chem. 1998 May 22; 273(21):13104-9. PMID: 9582349.
        View in: PubMed
      160. Sonenberg N, Burley S, Gingras AC. RNA chiropractics. Nat Struct Biol. 1998 Mar; 5(3):172-4. PMID: 9501904.
        View in: PubMed
      161. Cirillo LA, McPherson CE, Bossard P, Stevens K, Cherian S, Shim EY, Clark KL, Burley S, Zaret KS. Binding of the winged-helix transcription factor HNF3 to a linker histone site on the nucleosome. EMBO J. 1998 Jan 02; 17(1):244-54. PMID: 9427758; PMCID: PMC1170375.
      162. Burley S. X-ray crystallographic studies of eukaryotic transcription factors. Cold Spring Harb Symp Quant Biol. 1998; 63:33-40. PMID: 10384268.
        View in: PubMed
      163. Marcotrigiano J, Gingras AC, Sonenberg N, Burley S. Cocrystal structure of the messenger RNA 5' cap-binding protein (eIF4E) bound to 7-methyl-GDP. Cell. 1997 Jun 13; 89(6):951-61. PMID: 9200613.
        View in: PubMed
      164. Werner MH, Burley S. Architectural transcription factors: proteins that remodel DNA. Cell. 1997 Mar 21; 88(6):733-6. PMID: 9118214.
        View in: PubMed
      165. Burley S, Xie X, Clark KL, Shu F. Histone-like transcription factors in eukaryotes. Curr Opin Struct Biol. 1997 Feb; 7(1):94-102. PMID: 9032065.
        View in: PubMed
      166. Rhodes D, Burley S. Protein-nucleic acid interactions. Curr Opin Struct Biol. 1997 Feb; 7(1):73-5. PMID: 9032068.
        View in: PubMed
      167. Nikolov DB, Burley S. RNA polymerase II transcription initiation: a structural view. Proc Natl Acad Sci U S A. 1997 Jan 07; 94(1):15-22. PMID: 8990153; PMCID: PMC33652.
      168. Marcotrigiano J, Gingras AC, Sonenberg N, Burley S. X-ray studies of the messenger RNA 5' cap-binding protein (eIF4E) bound to 7-methyl-GDP. Nucleic Acids Symp Ser. 1997; (36):8-11. PMID: 9478191.
        View in: PubMed
      169. Patikoglou G, Burley S. Eukaryotic transcription factor-DNA complexes. Annu Rev Biophys Biomol Struct. 1997; 26:289-325. PMID: 9241421.
        View in: PubMed
      170. Houbaviy HB, Usheva A, Shenk T, Burley S. Cocrystal structure of YY1 bound to the adeno-associated virus P5 initiator. Proc Natl Acad Sci U S A. 1996 Nov 26; 93(24):13577-82. PMID: 8942976; PMCID: PMC19349.
      171. Steingrímsson E, Nii A, Fisher DE, Ferré-D'Amaré AR, McCormick RJ, Russell LB, Burley S, Ward JM, Jenkins NA, Copeland NG. The semidominant Mi(b) mutation identifies a role for the HLH domain in DNA binding in addition to its role in protein dimerization. EMBO J. 1996 Nov 15; 15(22):6280-9. PMID: 8947051; PMCID: PMC452451.
      172. Bryant GO, Martel LS, Burley S, Berk AJ. Radical mutations reveal TATA-box binding protein surfaces required for activated transcription in vivo. Genes Dev. 1996 Oct 01; 10(19):2491-504. PMID: 8843200.
        View in: PubMed
      173. Nikolov DB, Chen H, Halay ED, Hoffman A, Roeder RG, Burley S. Crystal structure of a human TATA box-binding protein/TATA element complex. Proc Natl Acad Sci U S A. 1996 May 14; 93(10):4862-7. PMID: 8643494; PMCID: PMC39370.
      174. Burley S. Picking up the TAB. Nature. 1996 May 09; 381(6578):112-3. PMID: 8610004.
        View in: PubMed
      175. Burley S. X-ray crystallographic studies of eukaryotic transcription initiation factors. Philos Trans R Soc Lond B Biol Sci. 1996 Apr 29; 351(1339):483-9. PMID: 8735270.
        View in: PubMed
      176. Xie X, Kokubo T, Cohen SL, Mirza UA, Hoffmann A, Chait BT, Roeder RG, Nakatani Y, Burley S. Structural similarity between TAFs and the heterotetrameric core of the histone octamer. Nature. 1996 Mar 28; 380(6572):316-22. PMID: 8598927.
        View in: PubMed
      177. Hoffmann A, Chiang CM, Oelgeschläger T, Xie X, Burley S, Nakatani Y, Roeder RG. A histone octamer-like structure within TFIID. Nature. 1996 Mar 28; 380(6572):356-9. PMID: 8598932.
        View in: PubMed
      178. Burley S. The TATA box binding protein. Curr Opin Struct Biol. 1996 Feb; 6(1):69-75. PMID: 8696975.
        View in: PubMed
      179. Burley S, Roeder RG. Biochemistry and structural biology of transcription factor IID (TFIID). Annu Rev Biochem. 1996; 65:769-99. PMID: 8811195.
        View in: PubMed
      180. Nikolov DB, Chen H, Halay ED, Usheva AA, Hisatake K, Lee DK, Roeder RG, Burley S. Crystal structure of a TFIIB-TBP-TATA-element ternary complex. Nature. 1995 Sep 14; 377(6545):119-28. PMID: 7675079.
        View in: PubMed
      181. Sha M, Ferré-D'Amaré AR, Burley S, Goss DJ. Anti-cooperative biphasic equilibrium binding of transcription factor upstream stimulatory factor to its cognate DNA monitored by protein fluorescence changes. J Biol Chem. 1995 Aug 18; 270(33):19325-9. PMID: 7642609.
        View in: PubMed
      182. Halaas JL, Gajiwala KS, Maffei M, Cohen SL, Chait BT, Rabinowitz D, Lallone RL, Burley S, Friedman JM. Weight-reducing effects of the plasma protein encoded by the obese gene. Science. 1995 Jul 28; 269(5223):543-6. PMID: 7624777.
        View in: PubMed
      183. Kim JL, Burley S. PCD/DCoH: more than a second molecular saddle. Structure. 1995 Jun 15; 3(6):531-4. PMID: 8590013.
        View in: PubMed
      184. Cohen SL, Ferré-D'Amaré AR, Burley S, Chait BT. Probing the solution structure of the DNA-binding protein Max by a combination of proteolysis and mass spectrometry. Protein Sci. 1995 Jun; 4(6):1088-99. PMID: 7549873; PMCID: PMC2143150.
      185. Burley S. Rel revealed: cocrystal structures of the NF-kappa B p50 homodimer. Chem Biol. 1995 Feb; 2(2):77-81. PMID: 9383407.
        View in: PubMed
      186. Steingrímsson E, Moore KJ, Lamoreux ML, Ferré-D'Amaré AR, Burley S, Zimring DC, Skow LC, Hodgkinson CA, Arnheiter H, Copeland NG. Molecular basis of mouse microphthalmia (mi) mutations helps explain their developmental and phenotypic consequences. Nat Genet. 1994 Nov; 8(3):256-63. PMID: 7874168.
        View in: PubMed
      187. Burley S. p53: a cellular Achilles' heel revealed. Structure. 1994 Sep 15; 2(9):789-92. PMID: 7812712.
        View in: PubMed
      188. Nikolov DB, Burley S. 2.1 A resolution refined structure of a TATA box-binding protein (TBP). Nat Struct Biol. 1994 Sep; 1(9):621-37. PMID: 7634102.
        View in: PubMed
      189. Kim JL, Burley S. 1.9 A resolution refined structure of TBP recognizing the minor groove of TATAAAAG. Nat Struct Biol. 1994 Sep; 1(9):638-53. PMID: 7634103.
        View in: PubMed
      190. Ferré-D'Amaré AR, Burley S. Use of dynamic light scattering to assess crystallizability of macromolecules and macromolecular assemblies. Structure. 1994 May 15; 2(5):357-9. PMID: 8081751.
        View in: PubMed
      191. Ferré-D'Amaré AR, Pognonec P, Roeder RG, Burley S. Structure and function of the b/HLH/Z domain of USF. EMBO J. 1994 Jan 01; 13(1):180-9. PMID: 8306960; PMCID: PMC394791.
      192. Lai E, Clark KL, Burley S, Darnell JE. Hepatocyte nuclear factor 3/fork head or "winged helix" proteins: a family of transcription factors of diverse biologic function. Proc Natl Acad Sci U S A. 1993 Nov 15; 90(22):10421-3. PMID: 8248124; PMCID: PMC47788.
      193. Kim JL, Nikolov DB, Burley S. Co-crystal structure of TBP recognizing the minor groove of a TATA element. Nature. 1993 Oct 07; 365(6446):520-7. PMID: 8413605.
        View in: PubMed
      194. Clark KL, Halay ED, Lai E, Burley S. Co-crystal structure of the HNF-3/fork head DNA-recognition motif resembles histone H5. Nature. 1993 Jul 29; 364(6436):412-20. PMID: 8332212.
        View in: PubMed
      195. Ferré-D'Amaré AR, Prendergast GC, Ziff EB, Burley S. Recognition by Max of its cognate DNA through a dimeric b/HLH/Z domain. Nature. 1993 May 06; 363(6424):38-45. PMID: 8479534.
        View in: PubMed
      196. Kim H, Burley S, Lipscomb WN. Re-refinement of the X-ray crystal structure of bovine lens leucine aminopeptidase complexed with bestatin. J Mol Biol. 1993 Apr 05; 230(3):722-4. PMID: 8478928.
        View in: PubMed
      197. Burley S, Clark KL, Ferré-D'Amaré A, Kim JL, Nikolov DB. X-ray crystallographic studies of eukaryotic transcription factors. Cold Spring Harb Symp Quant Biol. 1993; 58:123-32. PMID: 7956022.
        View in: PubMed
      198. Nikolov DB, Hu SH, Lin J, Gasch A, Hoffmann A, Horikoshi M, Chua NH, Roeder RG, Burley S. Crystal structure of TFIID TATA-box binding protein. Nature. 1992 Nov 05; 360(6399):40-6. PMID: 1436073.
        View in: PubMed
      199. Burley S, David PR, Sweet RM, Taylor A, Lipscomb WN. Structure determination and refinement of bovine lens leucine aminopeptidase and its complex with bestatin. J Mol Biol. 1992 Mar 05; 224(1):113-40. PMID: 1548695.
        View in: PubMed
      200. Burley S, David PR, Lipscomb WN. Leucine aminopeptidase: bestatin inhibition and a model for enzyme-catalyzed peptide hydrolysis. Proc Natl Acad Sci U S A. 1991 Aug 15; 88(16):6916-20. PMID: 1871107; PMCID: PMC52204.
      201. Kuriyan J, Osapay K, Burley S, Brünger AT, Hendrickson WA, Karplus M. Exploration of disorder in protein structures by X-ray restrained molecular dynamics. Proteins. 1991; 10(4):340-58. PMID: 1946343.
        View in: PubMed
      202. Burley S, David PR, Taylor A, Lipscomb WN. Molecular structure of leucine aminopeptidase at 2.7-A resolution. Proc Natl Acad Sci U S A. 1990 Sep; 87(17):6878-82. PMID: 2395881; PMCID: PMC54641.
      203. Burley S, Petsko GA. Weakly polar interactions in proteins. Adv Protein Chem. 1988; 39:125-89. PMID: 3072867.
        View in: PubMed
      204. Burley S, Wang AH, Votano JR, Rich A. Antigelling and antisickling bisphenyl oligopeptides and peptide analogues have similar structural features. Biochemistry. 1987 Aug 11; 26(16):5091-9. PMID: 3663644.
        View in: PubMed
      205. Burley S, Petsko GA. Amino-aromatic interactions in proteins. FEBS Lett. 1986 Jul 28; 203(2):139-43. PMID: 3089835.
        View in: PubMed
      206. Burley S, Petsko GA. Aromatic-aromatic interaction: a mechanism of protein structure stabilization. Science. 1985 Jul 05; 229(4708):23-8. PMID: 3892686.
        View in: PubMed