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Stephen Burley

Title(s)RES (WOS), CACSE
SchoolVc-academic Affairs
Address9500 Gilman Drive #
La Jolla CA 92093
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    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. to make corrections and additions.
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Matrix Metalloproteinases as Candidate Antigenic Determinants for Anti-Tumor Autoantibodies in Human Ovarian Cancer: A Post Hoc Analysis. FASEB J. 2025 Sep 30; 39(18):e71066. Markosian C, Ille AM, Burley SK, Arap W, Pasqualini R. PMID: 40985572; PMCID: PMC12455903.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    2. Human protein interactome structure prediction at scale with Boltz-2. bioRxiv. 2025 Aug 21. Ille AM, Markosian C, Burley SK, Pasqualini R, Arap W. PMID: 40631076; PMCID: PMC12236519.
      View in: PubMed   Mentions:
    3. Q-score as a reliability measure for protein, nucleic acid and small-molecule atomic coordinate models derived from 3DEM maps. Acta Crystallogr D Struct Biol. 2025 Aug 01; 81(Pt 8):410-422. Pintilie G, Shao C, Wang Z, Hudson BP, Flatt JW, Schmid MF, Morris KL, Burley SK, Chiu W. PMID: 40654171; PMCID: PMC12315582.
      View in: PubMed   Mentions: Translation:Cells
    4. MolViewSpec: a Mol* extension for describing and sharing molecular visualizations. Nucleic Acids Res. 2025 Jul 07; 53(W1):W408-W414. Midlik A, Bittrich S, Fleming JR, Nair S, Velankar S, Burley SK, Young JY, Vallat B, Sehnal D. PMID: 40326523; PMCID: PMC12230705.
      View in: PubMed   Mentions:    Fields:    
    5. Conformational ligand-directed targeting of calcium-dependent receptors in acute trauma. Med. 2025 Jul 11; 6(7):100638. Pasqualini R, Markosian C, Staquicini DI, Dobroff AS, Dodero-Rojas E, Whitford PC, Barbu EM, Bronk JK, Cardó-Vila M, Christianson DR, Dias-Neto E, Driessen WHP, Guzman-Rojas L, Marchiò S, Nunes DN, de Oliveira FS, Ozawa MG, Proneth B, Rangel R, Smith TL, Souza GR, Staquicini FI, Tang FHF, Baze WB, Setubal JC, Burns JW, Dubick MA, Gelovani JG, Batchinsky AI, Mogford JE, Wade CE, Holcomb JB, Burley SK, Onuchic JN, Arap W. PMID: 40609540.
      View in: PubMed   Mentions:    Fields:    Translation:AnimalsCells
    6. From sequence to protein structure and conformational dynamics with artificial intelligence/machine learning. Struct Dyn. 2025 May; 12(3):030902. Ille AM, Anas E, Mathews MB, Burley SK. PMID: 40567503; PMCID: PMC12195464.
      View in: PubMed   Mentions:
    7. Where and how to house big data on small fragments. Nat Commun. 2025 May 05; 16(1):4179. Erlanson DA, Burley SK, Fearon D, Fraser JS, Kreitler D, Nonato MC, Sakai N, Wollenhaupt J, Weiss MS. PMID: 40325009; PMCID: PMC12052810.
      View in: PubMed   Mentions: 1     Fields:    Translation:Humans
    8. High-throughput prediction of peptide structural conformations with AlphaFold2. bioRxiv. 2025 Apr 28. Ille AM, Markosian C, Burley SK, Whitford PC, Onuchic JN, Pasqualini R, Arap W. PMID: 39677766; PMCID: PMC11642853.
      View in: PubMed   Mentions:
    9. A new chapter for RCSB Protein Data Bank Molecule of the Month in 2025. Struct Dyn. 2025 Mar; 12(2):021101. Iwasa J, Goodsell DS, Burley SK, Zardecki C. PMID: 40255535; PMCID: PMC12009144.
      View in: PubMed   Mentions: 1  
    10. Visualizing and analyzing 3D biomolecular structures using Mol* at RCSB.org: Influenza A H5N1 virus proteome case study. Protein Sci. 2025 Apr; 34(4):e70093. Bittrich S, Rose AS, Sehnal D, Duarte JM, Rose Y, Segura J, Piehl DW, Vallat B, Shao C, Bhikadiya C, Liang J, Ma M, Goodsell DS, Burley SK, Dutta S. PMID: 40099807; PMCID: PMC11915458.
      View in: PubMed   Mentions:    Fields:    Translation:Cells
    11. Multi-scale structural similarity embedding search across entire proteomes. bioRxiv. 2025 Mar 06. Segura J, Sanchez-Garcia R, Bittrich S, Rose Y, Burley SK, Duarte JM. PMID: 40093062; PMCID: PMC11908163.
      View in: PubMed   Mentions:
    12. Protein Data Bank (PDB): Fifty-three years young and having a transformative impact on science and society. Q Rev Biophys. 2025 02 20; 58:e9. Berman HM, Burley SK. PMID: 39973356.
      View in: PubMed   Mentions: 5     Fields:    Translation:Humans
    13. rcsb-api: Python Toolkit for Streamlining Access to RCSB Protein Data Bank APIs. J Mol Biol. 2025 Aug 01; 437(15):168970. Piehl DW, Vallat B, Truong I, Morsy H, Bhatt R, Blaumann S, Biswas P, Rose Y, Bittrich S, Duarte JM, Segura J, Bi C, Myers-Turnbull D, Hudson BP, Zardecki C, Burley SK. PMID: 39894387.
      View in: PubMed   Mentions: 1     Fields:    Translation:Cells
    14. PDB-IHM: A System for Deposition, Curation, Validation, and Dissemination of Integrative Structures. J Mol Biol. 2025 Aug 01; 437(15):168963. Vallat B, Webb BM, Zalevsky A, Tangmunarunkit H, Sekharan MR, Voinea S, Shafaeibejestan A, Sagendorf J, Hoch JC, Kurisu G, Morris KL, Velankar S, Kesselman C, Burley SK, Berman HM, Sali A. PMID: 40110969; PMCID: PMC12327472.
      View in: PubMed   Mentions: 1     Fields:    Translation:Cells
    15. Q-score as a reliability measure for protein, nucleic acid, and small molecule atomic coordinate models derived from 3DEM density maps. bioRxiv. 2025 Jan 15. Pintilie G, Shao C, Wang Z, Hudson BP, Flatt JW, Schmid MF, Morris K, Burley SK, Chiu W. PMID: 39868161; PMCID: PMC11760781.
      View in: PubMed   Mentions:
    16. Updated resources for exploring experimentally-determined PDB structures and Computed Structure Models at the RCSB Protein Data Bank. Nucleic Acids Res. 2025 Jan 06; 53(D1):D564-D574. Burley SK, Bhatt R, Bhikadiya C, Bi C, Biester A, Biswas P, Bittrich S, Blaumann S, Brown R, Chao H, Chithari VR, Craig PA, Crichlow GV, Duarte JM, Dutta S, Feng Z, Flatt JW, Ghosh S, Goodsell DS, Green RK, Guranovic V, Henry J, Hudson BP, Joy M, Kaelber JT, Khokhriakov I, Lai JS, Lawson CL, Liang Y, Myers-Turnbull D, Peisach E, Persikova I, Piehl DW, Pingale A, Rose Y, Sagendorf J, Sali A, Segura J, Sekharan M, Shao C, Smith J, Trumbull M, Vallat B, Voigt M, Webb B, Whetstone S, Wu-Wu A, Xing T, Young JY, Zalevsky A, Zardecki C. PMID: 39607707; PMCID: PMC11701563.
      View in: PubMed   Mentions: 21     Fields:    Translation:HumansCells
    17. BindingDB in 2024: a FAIR knowledgebase of protein-small molecule binding data. Nucleic Acids Res. 2025 Jan 06; 53(D1):D1633-D1644. Liu T, Hwang L, Burley SK, Nitsche CI, Southan C, Walters WP, Gilson MK. PMID: 39574417; PMCID: PMC11701568.
      View in: PubMed   Mentions: 13     Fields:    Translation:HumansCells
    18. Protein data bank: From two epidemics to the global pandemic to mRNA vaccines and Paxlovid. Curr Opin Struct Biol. 2025 Feb; 90:102954. Burley SK. PMID: 39586184.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansCellsPHPublic Health
    19. Generative artificial intelligence performs rudimentary structural biology modeling. Sci Rep. 2024 08 21; 14(1):19372. Ille AM, Markosian C, Burley SK, Mathews MB, Pasqualini R, Arap W. PMID: 39169047; PMCID: PMC11339285.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansCells
    20. ZMPY3D: accelerating protein structure volume analysis through vectorized 3D Zernike moments and Python-based GPU integration. Bioinform Adv. 2024; 4(1):vbae111. Lai JS, Burley SK, Duarte JM. PMID: 39100546; PMCID: PMC11297494.
      View in: PubMed   Mentions:
    21. Describing and Sharing Molecular Visualizations Using the MolViewSpec Toolkit. Curr Protoc. 2024 Jul; 4(7):e1099. Bittrich S, Midlik A, Varadi M, Velankar S, Burley SK, Young JY, Sehnal D, Vallat B. PMID: 39024028; PMCID: PMC11338654.
      View in: PubMed   Mentions: 4     Fields:    
    22. Outcomes of the EMDataResource cryo-EM Ligand Modeling Challenge. Nat Methods. 2024 Jul; 21(7):1340-1348. Lawson CL, Kryshtafovych A, Pintilie GD, Burley SK, Cerný J, Chen VB, Emsley P, Gobbi A, Joachimiak A, Noreng S, Prisant MG, Read RJ, Richardson JS, Rohou AL, Schneider B, Sellers BD, Shao C, Sourial E, Williams CI, Williams CJ, Yang Y, Abbaraju V, Afonine PV, Baker ML, Bond PS, Blundell TL, Burnley T, Campbell A, Cao R, Cheng J, Chojnowski G, Cowtan KD, DiMaio F, Esmaeeli R, Giri N, Grubmüller H, Hoh SW, Hou J, Hryc CF, Hunte C, Igaev M, Joseph AP, Kao WC, Kihara D, Kumar D, Lang L, Lin S, Maddhuri Venkata Subramaniya SR, Mittal S, Mondal A, Moriarty NW, Muenks A, Murshudov GN, Nicholls RA, Olek M, Palmer CM, Perez A, Pohjolainen E, Pothula KR, Rowley CN, Sarkar D, Schäfer LU, Schlicksup CJ, Schröder GF, Shekhar M, Si D, Singharoy A, Sobolev OV, Terashi G, Vaiana AC, Vedithi SC, Verburgt J, Wang X, Warshamanage R, Winn MD, Weyand S, Yamashita K, Zhao M, Schmid MF, Berman HM, Chiu W. PMID: 38918604; PMCID: PMC11526832.
      View in: PubMed   Mentions: 8     Fields:    Translation:Cells
    23. Impact of structural biology and the protein data bank on us fda new drug approvals of low molecular weight antineoplastic agents 2019-2023. Oncogene. 2024 07; 43(29):2229-2243. Burley SK, Wu-Wu A, Dutta S, Ganesan S, Zheng SXF. PMID: 38886570; PMCID: PMC11245395.
      View in: PubMed   Mentions: 2     Fields:    Translation:Humans
    24. RCSB protein Data Bank: exploring protein 3D similarities via comprehensive structural alignments. Bioinformatics. 2024 06 03; 40(6). Bittrich S, Segura J, Duarte JM, Burley SK, Rose Y. PMID: 38870521; PMCID: PMC11212067.
      View in: PubMed   Mentions: 58     Fields:    Translation:Cells
    25. PDB NextGen Archive: centralizing access to integrated annotations and enriched structural information by the Worldwide Protein Data Bank. Database (Oxford). 2024 05 27; 2024. Choudhary P, Feng Z, Berrisford J, Chao H, Ikegawa Y, Peisach E, Piehl DW, Smith J, Tanweer A, Varadi M, Westbrook JD, Young JY, Patwardhan A, Morris KL, Hoch JC, Kurisu G, Velankar S, Burley SK. PMID: 38803272; PMCID: PMC11130521.
      View in: PubMed   Mentions: 5     Fields:    
    26. Generative artificial intelligence performs rudimentary structural biology modeling. bioRxiv. 2024 May 13. Ille AM, Markosian C, Burley SK, Mathews MB, Pasqualini R, Arap W. PMID: 38293060; PMCID: PMC10827103.
      View in: PubMed   Mentions:
    27. Nuclear mTOR Signaling Orchestrates Transcriptional Programs Underlying Cellular Growth and Metabolism. Cells. 2024 05 03; 13(9). Zhao T, Fan J, Abu-Zaid A, Burley SK, Zheng XFS. PMID: 38727317; PMCID: PMC11083943.
      View in: PubMed   Mentions: 8     Fields:    Translation:HumansAnimalsCells
    28. RCSB Protein Data Bank: supporting research and education worldwide through explorations of experimentally determined and computationally predicted atomic level 3D biostructures. IUCrJ. 2024 05 01; 11(Pt 3):279-286. Burley SK, Piehl DW, Vallat B, Zardecki C. PMID: 38597878; PMCID: PMC11067742.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansCells
    29. IHMCIF: An Extension of the PDBx/mmCIF Data Standard for Integrative Structure Determination Methods. J Mol Biol. 2024 Sep 01; 436(17):168546. Vallat B, Webb BM, Westbrook JD, Goddard TD, Hanke CA, Graziadei A, Peisach E, Zalevsky A, Sagendorf J, Tangmunarunkit H, Voinea S, Sekharan M, Yu J, Bonvin AAMJJ, DiMaio F, Hummer G, Meiler J, Tajkhorshid E, Ferrin TE, Lawson CL, Leitner A, Rappsilber J, Seidel CAM, Jeffries CM, Burley SK, Hoch JC, Kurisu G, Morris K, Patwardhan A, Velankar S, Schwede T, Trewhella J, Kesselman C, Berman HM, Sali A. PMID: 38508301; PMCID: PMC11377171.
      View in: PubMed   Mentions: 2     Fields:    Translation:Cells
    30. Restraint validation of biomolecular structures determined by NMR in the Protein Data Bank. Structure. 2024 06 06; 32(6):824-837.e1. Baskaran K, Ploskon E, Tejero R, Yokochi M, Harrus D, Liang Y, Peisach E, Persikova I, Ramelot TA, Sekharan M, Tolchard J, Westbrook JD, Bardiaux B, Schwieters CD, Patwardhan A, Velankar S, Burley SK, Kurisu G, Hoch JC, Montelione GT, Vuister GW, Young JY. PMID: 38490206; PMCID: PMC11162339.
      View in: PubMed   Mentions: 3     Fields:    Translation:Cells
    31. Community recommendations on cryoEM data archiving and validation. IUCrJ. 2024 03 01; 11(Pt 2):140-151. Kleywegt GJ, Adams PD, Butcher SJ, Lawson CL, Rohou A, Rosenthal PB, Subramaniam S, Topf M, Abbott S, Baldwin PR, Berrisford JM, Bricogne G, Choudhary P, Croll TI, Danev R, Ganesan SJ, Grant T, Gutmanas A, Henderson R, Heymann JB, Huiskonen JT, Istrate A, Kato T, Lander GC, Lok SM, Ludtke SJ, Murshudov GN, Pye R, Pintilie GD, Richardson JS, Sachse C, Salih O, Scheres SHW, Schroeder GF, Sorzano COS, Stagg SM, Wang Z, Warshamanage R, Westbrook JD, Winn MD, Young JY, Burley SK, Hoch JC, Kurisu G, Morris K, Patwardhan A, Velankar S. PMID: 38358351; PMCID: PMC10916293.
      View in: PubMed   Mentions: 10     Fields:    
    32. Folding paper models of biostructures for outreach and education. Patterns (N Y). 2024 Feb 09; 5(2):100931. Goodsell DS, Dutta S, Hudson BP, Voigt M, Burley SK, Zardecki C. PMID: 38370120; PMCID: PMC10873190.
      View in: PubMed   Mentions:
    33. Community recommendations on cryoEM data archiving and validation: Outcomes of a wwPDB/EMDB workshop on cryoEM data management, deposition and validation. ArXiv. 2024 Feb 02. Kleywegt GJ, Adams PD, Butcher SJ, Lawson CL, Rohou A, Rosenthal PB, Subramaniam S, Topf M, Abbott S, Baldwin PR, Berrisford JM, Bricogne G, Choudhary P, Croll TI, Danev R, Ganesan SJ, Grant T, Gutmanas A, Henderson R, Heymann JB, Huiskonen JT, Istrate A, Kato T, Lander GC, Lok SM, Ludtke SJ, Murshudov GN, Pye R, Pintilie GD, Richardson JS, Sachse C, Salih O, Scheres SHW, Schroeder GF, Sorzano COS, Stagg SM, Wang Z, Warshamanage R, Westbrook JD, Winn MD, Young JY, Burley SK, Hoch JC, Kurisu G, Morris K, Patwardhan A, Velankar S. PMID: 38076521; PMCID: PMC10705588.
      View in: PubMed   Mentions:
    34. Outcomes of the EMDataResource Cryo-EM Ligand Modeling Challenge. Res Sq. 2024 Jan 25. Lawson CL, Kryshtafovych A, Pintilie GD, Burley SK, Cerný J, Chen VB, Emsley P, Gobbi A, Joachimiak A, Noreng S, Prisant M, Read RJ, Richardson JS, Rohou AL, Schneider B, Sellers BD, Shao C, Sourial E, Williams CI, Williams CJ, Yang Y, Abbaraju V, Afonine PV, Baker ML, Bond PS, Blundell TL, Burnley T, Campbell A, Cao R, Cheng J, Chojnowski G, Cowtan KD, DiMaio F, Esmaeeli R, Giri N, Grubmüller H, Hoh SW, Hou J, Hryc CF, Hunte C, Igaev M, Joseph AP, Kao WC, Kihara D, Kumar D, Lang L, Lin S, Maddhuri Venkata Subramaniya SR, Mittal S, Mondal A, Moriarty NW, Muenks A, Murshudov GN, Nicholls RA, Olek M, Palmer CM, Perez A, Pohjolainen E, Pothula KR, Rowley CN, Sarkar D, Schäfer LU, Schlicksup CJ, Schröder GF, Shekhar M, Si D, Singharoy A, Sobolev OV, Terashi G, Vaiana AC, Vedithi SC, Verburgt J, Wang X, Warshamanage R, Winn MD, Weyand S, Yamashita K, Zhao M, Schmid MF, Berman HM, Chiu W. PMID: 38343795; PMCID: PMC10854310.
      View in: PubMed   Mentions:
    35. Restraint Validation of Biomolecular Structures Determined by NMR in the Protein Data Bank. bioRxiv. 2024 Jan 22. Baskaran K, Ploskon E, Tejero R, Yokochi M, Harrus D, Liang Y, Peisach E, Persikova I, Ramelot TA, Sekharan M, Tolchard J, Westbrook JD, Bardiaux B, Schwieters CD, Patwardhan A, Velankar S, Burley SK, Kurisu G, Hoch JC, Montelione GT, Vuister GW, Young JY. PMID: 38328042; PMCID: PMC10849500.
      View in: PubMed   Mentions:
    36. RCSB Protein Data Bank: visualizing groups of experimentally determined PDB structures alongside computed structure models of proteins. Front Bioinform. 2023; 3:1311287. Segura J, Rose Y, Bi C, Duarte J, Burley SK, Bittrich S. PMID: 38111685; PMCID: PMC10726007.
      View in: PubMed   Mentions: 1  
    37. The next decade in structural biology. Structure. 2023 11 02; 31(11):1284-1288. Walsh MA, Nannenga BL, Gonen T, Sexton PM, Wootten D, Chiu W, Sun F, Carragher B, Potter CS, Agard D, Burley SK. PMID: 37922863.
      View in: PubMed   Mentions:    Fields:    
    38. Announcing the launch of Protein Data Bank China as an Associate Member of the Worldwide Protein Data Bank Partnership. Acta Crystallogr D Struct Biol. 2023 Sep 01; 79(Pt 9):792-795. Xu W, Velankar S, Patwardhan A, Hoch JC, Burley SK, Kurisu G. PMID: 37561405; PMCID: PMC10478634.
      View in: PubMed   Mentions: 10  Translation:HumansCells
    39. Modeling of ACE2 and antibodies bound to SARS-CoV-2 provides insights into infectivity and immune evasion. JCI Insight. 2023 07 10; 8(13). Lubin JH, Markosian C, Balamurugan D, Ma MT, Chen CH, Liu D, Pasqualini R, Arap W, Burley SK, Khare SD. PMID: 37261904; PMCID: PMC10371346.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansCellsPHPublic Health
    40. ModelCIF: An Extension of PDBx/mmCIF Data Representation for Computed Structure Models. J Mol Biol. 2023 07 15; 435(14):168021. Vallat B, Tauriello G, Bienert S, Haas J, Webb BM, Žídek A, Zheng W, Peisach E, Piehl DW, Anischanka I, Sillitoe I, Tolchard J, Varadi M, Baker D, Orengo C, Zhang Y, Hoch JC, Kurisu G, Patwardhan A, Velankar S, Burley SK, Sali A, Schwede T, Berman HM, Westbrook JD. PMID: 36828268; PMCID: PMC10293049.
      View in: PubMed   Mentions: 10     Fields:    Translation:Cells
    41. RCSB Protein Data Bank: Efficient Searching and Simultaneous Access to One Million Computed Structure Models Alongside the PDB Structures Enabled by Architectural Advances. J Mol Biol. 2023 07 15; 435(14):167994. Bittrich S, Bhikadiya C, Bi C, Chao H, Duarte JM, Dutta S, Fayazi M, Henry J, Khokhriakov I, Lowe R, Piehl DW, Segura J, Vallat B, Voigt M, Westbrook JD, Burley SK, Rose Y. PMID: 36738985; PMCID: PMC11514064.
      View in: PubMed   Mentions: 18     Fields:    Translation:HumansCells
    42. A comprehensive survey of coronaviral main protease active site diversity in 3D: Identifying and analyzing drug discovery targets in search of broad specificity inhibitors for the next coronavirus pandemic. bioRxiv. 2023 Jan 31. Lubin JH, Martinusen SG, Zardecki C, Olivas C, Bacorn M, Balogun M, Slaton EW, Wu AW, Sakeer S, Hudson BP, Denard CA, Burley SK, Khare SD. PMID: 36778399; PMCID: PMC9915488.
      View in: PubMed   Mentions:
    43. RCSB Protein Data Bank (RCSB.org): delivery of experimentally-determined PDB structures alongside one million computed structure models of proteins from artificial intelligence/machine learning. Nucleic Acids Res. 2023 01 06; 51(D1):D488-D508. Burley SK, Bhikadiya C, Bi C, Bittrich S, Chao H, Chen L, Craig PA, Crichlow GV, Dalenberg K, Duarte JM, Dutta S, Fayazi M, Feng Z, Flatt JW, Ganesan S, Ghosh S, Goodsell DS, Green RK, Guranovic V, Henry J, Hudson BP, Khokhriakov I, Lawson CL, Liang Y, Lowe R, Peisach E, Persikova I, Piehl DW, Rose Y, Sali A, Segura J, Sekharan M, Shao C, Vallat B, Voigt M, Webb B, Westbrook JD, Whetstone S, Young JY, Zalevsky A, Zardecki C. PMID: 36420884; PMCID: PMC9825554.
      View in: PubMed   Mentions: 286     Fields:    Translation:Cells
    44. An idea to explore: How an interdisciplinary undergraduate course exploring a global health challenge in molecular detail enabled science communication and collaboration in diverse audiences. Biochem Mol Biol Educ. 2023 03; 51(2):137-145. Dutta S, Jiang J, Ghosh S, Patel S, Bhikadiya C, Lowe R, Voigt M, Goodsell D, Zardecki C, Burley SK. PMID: 36495283; PMCID: PMC10050141.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    45. Electron microscopy holdings of the Protein Data Bank: the impact of the resolution revolution, new validation tools, and implications for the future. Biophys Rev. 2022 Dec; 14(6):1281-1301. Burley SK, Berman HM, Chiu W, Dai W, Flatt JW, Hudson BP, Kaelber JT, Khare SD, Kulczyk AW, Lawson CL, Pintilie GD, Sali A, Vallat B, Westbrook JD, Young JY, Zardecki C. PMID: 36474933; PMCID: PMC9715422.
      View in: PubMed   Mentions: 25  
    46. RCSB Protein Data bank: Tools for visualizing and understanding biological macromolecules in 3D. Protein Sci. 2022 12; 31(12):e4482. Burley SK, Bhikadiya C, Bi C, Bittrich S, Chao H, Chen L, Craig PA, Crichlow GV, Dalenberg K, Duarte JM, Dutta S, Fayazi M, Feng Z, Flatt JW, Ganesan SJ, Ghosh S, Goodsell DS, Green RK, Guranovic V, Henry J, Hudson BP, Khokhriakov I, Lawson CL, Liang Y, Lowe R, Peisach E, Persikova I, Piehl DW, Rose Y, Sali A, Segura J, Sekharan M, Shao C, Vallat B, Voigt M, Webb B, Westbrook JD, Whetstone S, Young JY, Zalevsky A, Zardecki C. PMID: 36281733; PMCID: PMC9667899.
      View in: PubMed   Mentions: 33     Fields:    Translation:HumansCells
    47. Protein Data Bank: A Comprehensive Review of 3D Structure Holdings and Worldwide Utilization by Researchers, Educators, and Students. Biomolecules. 2022 10 04; 12(10). Burley SK, Berman HM, Duarte JM, Feng Z, Flatt JW, Hudson BP, Lowe R, Peisach E, Piehl DW, Rose Y, Sali A, Sekharan M, Shao C, Vallat B, Voigt M, Westbrook JD, Young JY, Zardecki C. PMID: 36291635; PMCID: PMC9599165.
      View in: PubMed   Mentions: 37     Fields:    Translation:HumansCells
    48. Exploring protein symmetry at the RCSB Protein Data Bank. Emerg Top Life Sci. 2022 09 09; 6(3):231-243. Duarte JM, Dutta S, Goodsell DS, Burley SK. PMID: 35801924; PMCID: PMC9472815.
      View in: PubMed   Mentions: 5     Fields:    
    49. Assessing PDB macromolecular crystal structure confidence at the individual amino acid residue level. Structure. 2022 10 06; 30(10):1385-1394.e3. Shao C, Bittrich S, Wang S, Burley SK. PMID: 36049478; PMCID: PMC9547844.
      View in: PubMed   Mentions: 23     Fields:    Translation:HumansCells
    50. A roadmap for the functional annotation of protein families: a community perspective. Database (Oxford). 2022 08 12; 2022. de Crécy-Lagard V, Amorin de Hegedus R, Arighi C, Babor J, Bateman A, Blaby I, Blaby-Haas C, Bridge AJ, Burley SK, Cleveland S, Colwell LJ, Conesa A, Dallago C, Danchin A, de Waard A, Deutschbauer A, Dias R, Ding Y, Fang G, Friedberg I, Gerlt J, Goldford J, Gorelik M, Gyori BM, Henry C, Hutinet G, Jaroch M, Karp PD, Kondratova L, Lu Z, Marchler-Bauer A, Martin MJ, McWhite C, Moghe GD, Monaghan P, Morgat A, Mungall CJ, Natale DA, Nelson WC, O'Donoghue S, Orengo C, O'Toole KH, Radivojac P, Reed C, Roberts RJ, Rodionov D, Rodionova IA, Rudolf JD, Saleh L, Sheynkman G, Thibaud-Nissen F, Thomas PD, Uetz P, Vallenet D, Carter EW, Weigele PR, Wood V, Wood-Charlson EM, Xu J. PMID: 35961013; PMCID: PMC9374478.
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    66. Modernized uniform representation of carbohydrate molecules in the Protein Data Bank. Glycobiology. 2021 09 20; 31(9):1204-1218. Shao C, Feng Z, Westbrook JD, Peisach E, Berrisford J, Ikegawa Y, Kurisu G, Velankar S, Burley SK, Young JY. PMID: 33978738; PMCID: PMC8457362.
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    108. Comparison of Alicyclobacillus acidocaldarius o-Succinylbenzoate Synthase to Its Promiscuous N-Succinylamino Acid Racemase/ o-Succinylbenzoate Synthase Relatives. Biochemistry. 2018 07 03; 57(26):3676-3689. Odokonyero D, McMillan AW, Ramagopal UA, Toro R, Truong DP, Zhu M, Lopez MS, Somiari B, Herman M, Aziz A, Bonanno JB, Hull KG, Burley SK, Romo D, Almo SC, Glasner ME. PMID: 29767960; PMCID: PMC7187728.
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    109. SOD1 Phosphorylation by mTORC1 Couples Nutrient Sensing and Redox Regulation. Mol Cell. 2018 05 03; 70(3):502-515.e8. Tsang CK, Chen M, Cheng X, Qi Y, Chen Y, Das I, Li X, Vallat B, Fu LW, Qian CN, Wang HY, White E, Burley SK, Zheng XFS. PMID: 29727620; PMCID: PMC6108545.
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    123. A public database of macromolecular diffraction experiments. Acta Crystallogr D Struct Biol. 2016 11 01; 72(Pt 11):1181-1193. Grabowski M, Langner KM, Cymborowski M, Porebski PJ, Sroka P, Zheng H, Cooper DR, Zimmerman MD, Elsliger MA, Burley SK, Minor W. PMID: 27841751; PMCID: PMC5108346.
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    127. Integrating genomic information with protein sequence and 3D atomic level structure at the RCSB protein data bank. Bioinformatics. 2016 12 15; 32(24):3833-3835. Prlic A, Kalro T, Bhattacharya R, Christie C, Burley SK, Rose PW. PMID: 27551105; PMCID: PMC5167066.
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    129. DCC: a Swiss army knife for structure factor analysis and validation. J Appl Crystallogr. 2016 Jun 01; 49(Pt 3):1081-1084. Yang H, Peisach E, Westbrook JD, Young J, Berman HM, Burley SK. PMID: 27275151; PMCID: PMC4886994.
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    131. Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop. Structure. 2015 Jul 07; 23(7):1156-67. Sali A, Berman HM, Schwede T, Trewhella J, Kleywegt G, Burley SK, 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. PMID: 26095030; PMCID: PMC4933300.
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    133. Identification of a Non-Gatekeeper Hot Spot for Drug-Resistant Mutations in mTOR Kinase. Cell Rep. 2015 Apr 21; 11(3):446-59. Wu TJ, Wang X, Zhang Y, Meng L, Kerrigan JE, Burley SK, Zheng XF. PMID: 25865887; PMCID: PMC4761412.
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    136. Crystal structure of Clostridium acetobutylicum Aspartate kinase (CaAK): An important allosteric enzyme for amino acids production. Biotechnol Rep (Amst). 2014 Sep 01; 3:73-85. Manjasetty BA, Chance MR, Burley SK, Panjikar S, Almo SC. PMID: 25170437; PMCID: PMC4142519.
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    137. 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. 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 SK, Chait BT, Almo SC, Rout MP, Sali A. PMID: 25139911; PMCID: PMC4223481.
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    138. 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. Korczynska M, Xiang DF, Zhang Z, Xu C, Narindoshvili T, Kamat SS, Williams HJ, Chang SS, Kolb P, Hillerich B, Sauder JM, Burley SK, Almo SC, Swaminathan S, Shoichet BK, Raushel FM. PMID: 24955762; PMCID: PMC4108184.
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    139. 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. 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 SK, Almo SC, Glasner ME. PMID: 24872444; PMCID: PMC4060685.
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    140. Revealing structural views of biology. Biopolymers. 2013 Nov; 99(11):817-24. Goodsell DS, Burley SK, Berman HM. PMID: 23821527.
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    141. Divergent evolution of ligand binding in the o-succinylbenzoate synthase family. Biochemistry. 2013 Oct 22; 52(42):7512-21. Odokonyero D, Ragumani S, Lopez MS, Bonanno JB, Ozerova ND, Woodard DR, Machala BW, Swaminathan S, Burley SK, Almo SC, Glasner ME. PMID: 24060347; PMCID: PMC3908897.
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    142. 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. Daughtry KD, Huang H, Malashkevich V, Patskovsky Y, Liu W, Ramagopal U, Sauder JM, Burley SK, Almo SC, Dunaway-Mariano D, Allen KN. PMID: 23848398; PMCID: PMC3966652.
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    144. Structure, dynamics, evolution, and function of a major scaffold component in the nuclear pore complex. Structure. 2013 Apr 02; 21(4):560-71. 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 SK, Sali A, Rout MP, Almo SC. PMID: 23499021; PMCID: PMC3755625.
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    145. PDB40: The Protein Data Bank celebrates its 40th birthday. Biopolymers. 2013 Mar; 99(3):165-7. Burley SK. PMID: 23280389.
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    146. A public-private partnership to unlock the untargeted kinome. Nat Chem Biol. 2013 Jan; 9(1):3-6. 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. PMID: 23238671.
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    148. 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. Palani K, Kumaran D, Burley SK, Swaminathan S. PMID: 23192024; PMCID: PMC3509965.
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    149. 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. Warlick BP, Evans BS, Erb TJ, Ramagopal UA, Sriram J, Imker HJ, Sauder JM, Bonanno JB, Burley SK, Tabita FR, Almo SC, Sweedler JS, Gerlt JA. PMID: 23035785; PMCID: PMC3490199.
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    150. Cas5d processes pre-crRNA and is a member of a larger family of CRISPR RNA endonucleases. RNA. 2012 Nov; 18(11):2020-8. Garside EL, Schellenberg MJ, Gesner EM, Bonanno JB, Sauder JM, Burley SK, Almo SC, Mehta G, MacMillan AM. PMID: 23006625; PMCID: PMC3479392.
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    152. Rapid-access, high-throughput synchrotron crystallography for drug discovery. Trends Pharmacol Sci. 2012 May; 33(5):261-7. Wasserman SR, Koss JW, Sojitra ST, Morisco LL, Burley SK. PMID: 22521107.
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    154. Structural insight into mechanism and diverse substrate selection strategy of L-ribulokinase. Proteins. 2012 Jan; 80(1):261-8. Agarwal R, Burley SK, Swaminathan S. PMID: 22072612; PMCID: PMC3240725.
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    156. Structural variation in bacterial glyoxalase I enzymes: investigation of the metalloenzyme glyoxalase I from Clostridium acetobutylicum. J Biol Chem. 2011 Nov 04; 286(44):38367-38374. Suttisansanee U, Lau K, Lagishetty S, Rao KN, Swaminathan S, Sauder JM, Burley SK, Honek JF. PMID: 21914803; PMCID: PMC3207458.
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    157. Gimme phospho-serine five! Capping enzyme guanylyltransferase recognition of the RNA polymerase II CTD. Mol Cell. 2011 Jul 22; 43(2):163-5. Burley SK, Sonenberg N. PMID: 21777807.
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    163. Catalytic mechanism and three-dimensional structure of adenine deaminase. Biochemistry. 2011 Mar 22; 50(11):1917-27. Kamat SS, Bagaria A, Kumaran D, Holmes-Hampton GP, Fan H, Sali A, Sauder JM, Burley SK, Lindahl PA, Swaminathan S, Raushel FM. PMID: 21247091; PMCID: PMC3059353.
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    164. Enzymatic deamination of the epigenetic base N-6-methyladenine. J Am Chem Soc. 2011 Feb 23; 133(7):2080-3. Kamat SS, Fan H, Sauder JM, Burley SK, Shoichet BK, Sali A, Raushel FM. PMID: 21275375; PMCID: PMC3043370.
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    165. 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. Zhang Z, Zhou R, Sauder JM, Tonge PJ, Burley SK, Swaminathan S. PMID: 21185305; PMCID: PMC3040979.
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    166. ModBase, a database of annotated comparative protein structure models, and associated resources. Nucleic Acids Res. 2011 Jan; 39(Database issue):D465-74. 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 SK, Sali A. PMID: 21097780; PMCID: PMC3013688.
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    167. Structural underpinnings of nitrogen regulation by the prototypical nitrogen-responsive transcriptional factor NrpR. Structure. 2010 Nov 10; 18(11):1512-21. Wisedchaisri G, Dranow DM, Lie TJ, Bonanno JB, Patskovsky Y, Ozyurt SA, Sauder JM, Almo SC, Wasserman SR, Burley SK, Leigh JA, Gonen T. PMID: 21070950; PMCID: PMC2996049.
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    168. 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. 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 SK. PMID: 20737437; PMCID: PMC2989796.
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    169. 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. Kikani CK, Antonysamy SA, Bonanno JB, Romero R, Zhang FF, Russell M, Gheyi T, Iizuka M, Emtage S, Sauder JM, Turk BE, Burley SK, Rutter J. PMID: 20943661; PMCID: PMC3003402.
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    170. Functional identification and structure determination of two novel prolidases from cog1228 in the amidohydrolase superfamily . Biochemistry. 2010 Aug 10; 49(31):6791-803. Xiang DF, Patskovsky Y, Xu C, Fedorov AA, Fedorov EV, Sisco AA, Sauder JM, Burley SK, Almo SC, Raushel FM. PMID: 20604542; PMCID: PMC2914802.
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    171. 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. Gheyi T, Rodgers L, Romero R, Sauder JM, Burley SK. PMID: 20685133; PMCID: PMC2963156.
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    172. Structures of the autoproteolytic domain from the Saccharomyces cerevisiae nuclear pore complex component, Nup145. Proteins. 2010 Jun; 78(8):1992-8. 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 SK. PMID: 20310066; PMCID: PMC3136511.
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    173. Discovery and structure determination of the orphan enzyme isoxanthopterin deaminase . Biochemistry. 2010 May 25; 49(20):4374-82. Hall RS, Agarwal R, Hitchcock D, Sauder JM, Burley SK, Swaminathan S, Raushel FM. PMID: 20415463; PMCID: PMC2892419.
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    174. The hunt for 8-oxoguanine deaminase. J Am Chem Soc. 2010 Feb 17; 132(6):1762-3. Hall RS, Fedorov AA, Marti-Arbona R, Fedorov EV, Kolb P, Sauder JM, Burley SK, Shoichet BK, Almo SC, Raushel FM. PMID: 20088583; PMCID: PMC2820149.
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    175. 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. 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 SK. PMID: 20156452; PMCID: PMC2881670.
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    176. Structural studies on cytosolic domain of magnesium transporter MgtE from Enterococcus faecalis. Proteins. 2010 Feb 01; 78(2):487-91. Ragumani S, Sauder JM, Burley SK, Swaminathan S. PMID: 19787770; PMCID: PMC3221319.
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    177. Safeguarding the integrity of protein archive. Nature. 2010 Jan 28; 463(7280):425. Berman HM, Kleywegt GJ, Nakamura H, Markley JL, Burley SK. PMID: 20110969; PMCID: PMC4456675.
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    178. 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. Lakshminarasimhan D, Eswaramoorthy S, Burley SK, Swaminathan S. PMID: 20057058; PMCID: PMC2805524.
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    179. 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. Rakus JF, Kalyanaraman C, Fedorov AA, Fedorov EV, Mills-Groninger FP, Toro R, Bonanno J, Bain K, Sauder JM, Burley SK, Almo SC, Jacobson MP, Gerlt JA. PMID: 19883118; PMCID: PMC2787699.
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    180. 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. 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 SK, Reich SH. PMID: 19934279.
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    181. Blocking UV-induced eIF2alpha phosphorylation with small molecule inhibitors of GCN2. Chem Biol Drug Des. 2009 Jul; 74(1):57-67. Robert F, Williams C, Yan Y, Donohue E, Cencic R, Burley SK, Pelletier J. PMID: 19519745; PMCID: PMC8221234.
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    182. Functional annotation of two new carboxypeptidases from the amidohydrolase superfamily of enzymes. Biochemistry. 2009 Jun 02; 48(21):4567-76. Xiang DF, Xu C, Kumaran D, Brown AC, Sauder JM, Burley SK, Swaminathan S, Raushel FM. PMID: 19358546; PMCID: PMC2748308.
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    183. Functional identification of incorrectly annotated prolidases from the amidohydrolase superfamily of enzymes. Biochemistry. 2009 May 05; 48(17):3730-42. Xiang DF, Patskovsky Y, Xu C, Meyer AJ, Sauder JM, Burley SK, Almo SC, Raushel FM. PMID: 19281183; PMCID: PMC2683473.
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    184. 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. Leiman PG, Basler M, Ramagopal UA, Bonanno JB, Sauder JM, Pukatzki S, Burley SK, Almo SC, Mekalanos JJ. PMID: 19251641; PMCID: PMC2657435.
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    185. 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. Sakai A, Fedorov AA, Fedorov EV, Schnoes AM, Glasner ME, Brown S, Rutter ME, Bain K, Chang S, Gheyi T, Sauder JM, Burley SK, Babbitt PC, Almo SC, Gerlt JA. PMID: 19220063; PMCID: PMC2746992.
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    186. Target selection and annotation for the structural genomics of the amidohydrolase and enolase superfamilies. J Struct Funct Genomics. 2009 Apr; 10(2):107-25. Pieper U, Chiang R, Seffernick JJ, Brown SD, Glasner ME, Kelly L, Eswar N, Sauder JM, Bonanno JB, Swaminathan S, Burley SK, Zheng X, Chance MR, Almo SC, Gerlt JA, Raushel FM, Jacobson MP, Babbitt PC, Sali A. PMID: 19219566; PMCID: PMC2693957.
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    187. Outcome of a workshop on applications of protein models in biomedical research. Structure. 2009 Feb 13; 17(2):151-9. 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. PMID: 19217386; PMCID: PMC2739730.
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    188. 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. Rao KN, Burley SK, Swaminathan S. PMID: 19079550; PMCID: PMC2596488.
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    189. Crystal structure of a putative lysostaphin peptidase from Vibrio cholerae. Proteins. 2008 Aug 15; 72(3):1096-103. Ragumani S, Kumaran D, Burley SK, Swaminathan S. PMID: 18498110; PMCID: PMC3614409.
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    190. X-ray crystal structure of the B component of Hemolysin BL from Bacillus cereus. Proteins. 2008 May 01; 71(2):534-40. Madegowda M, Eswaramoorthy S, Burley SK, Swaminathan S. PMID: 18175317; PMCID: PMC3220058.
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    191. 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. Agarwal R, Burley SK, Swaminathan S. PMID: 18247349.
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    192. A common catalytic mechanism for proteins of the HutI family. Biochemistry. 2008 May 20; 47(20):5608-15. Tyagi R, Eswaramoorthy S, Burley SK, Raushel FM, Swaminathan S. PMID: 18442260; PMCID: PMC3232013.
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    193. 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. O'Hare T, Eide CA, Tyner JW, Corbin AS, Wong MJ, Buchanan S, Holme K, Jessen KA, Tang C, Lewis HA, Romero RD, Burley SK, Deininger MW. PMID: 18367669; PMCID: PMC2291110.
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    194. Protein production and purification. Nat Methods. 2008 Feb; 5(2):135-46. Structural Genomics Consortium, China Structural Genomics Consortium, Northeast Structural Genomics Consortium, 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 SK, 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. PMID: 18235434; PMCID: PMC3178102.
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    195. Structure of human dual specificity protein phosphatase 23, VHZ, enzyme-substrate/product complex. J Biol Chem. 2008 Apr 04; 283(14):8946-53. Agarwal R, Burley SK, Swaminathan S. PMID: 18245086.
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    196. Crystal structure of a conserved protein of unknown function (MJ1651) from Methanococcus jannaschii. Proteins. 2008 Feb 01; 70(2):572-7. Rao KN, Burley SK, Swaminathan S. PMID: 17910070.
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    197. Contributions to the NIH-NIGMS Protein Structure Initiative from the PSI Production Centers. Structure. 2008 Jan; 16(1):5-11. Burley SK, Joachimiak A, Montelione GT, Wilson IA. PMID: 18184575; PMCID: PMC2678832.
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    198. High throughput protein production and crystallization at NYSGXRC. Methods Mol Biol. 2008; 426:561-75. Sauder MJ, Rutter ME, Bain K, Rooney I, Gheyi T, Atwell S, Thompson DA, Emtage S, Burley SK. PMID: 18542890.
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    199. Structural genomics of protein phosphatases. J Struct Funct Genomics. 2007 Sep; 8(2-3):121-40. 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 SK. PMID: 18058037; PMCID: PMC4163028.
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    200. X-ray structure of imidazolonepropionase from Agrobacterium tumefaciens at 1.87 A resolution. Proteins. 2007 Nov 15; 69(3):652-8. Tyagi R, Kumaran D, Burley SK, Swaminathan S. PMID: 17640072.
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    201. 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. Tyagi R, Burley SK, Swaminathan S. PMID: 17908300; PMCID: PMC2174479.
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    202. 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. Agarwal R, Burley SK, Swaminathan S. PMID: 17362992.
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    203. 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. Sabini E, Hazra S, Konrad M, Burley SK, Lavie A. PMID: 17158155; PMCID: PMC1802566.
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    204. Crystal structure of glycerophosphodiester phosphodiesterase from Agrobacterium tumefaciens by SAD with a large asymmetric unit. Proteins. 2006 Nov 01; 65(2):514-8. Rao KN, Bonanno JB, Burley SK, Swaminathan S. PMID: 16909422.
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    205. 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. Kumaran D, Bonanno JB, Burley SK, Swaminathan S. PMID: 16838328.
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    206. Outcome of a workshop on archiving structural models of biological macromolecules. Structure. 2006 Aug; 14(8):1211-7. Berman HM, Burley SK, Chiu W, Sali A, Adzhubei A, Bourne PE, Bryant SH, Dunbrack RL, Fidelis K, Frank J, Godzik A, Henrick K, Joachimiak A, Heymann B, Jones D, Markley JL, Moult J, Montelione GT, Orengo C, Rossmann MG, Rost B, Saibil H, Schwede T, Standley DM, Westbrook JD. PMID: 16955948.
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    207. Crystal structure of trehalose-6-phosphate phosphatase-related protein: biochemical and biological implications. Protein Sci. 2006 Jul; 15(7):1735-44. Rao KN, Kumaran D, Seetharaman J, Bonanno JB, Burley SK, Swaminathan S. PMID: 16815921; PMCID: PMC2242562.
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    208. Mechanism of action of a flavin-containing monooxygenase. Proc Natl Acad Sci U S A. 2006 Jun 27; 103(26):9832-7. Eswaramoorthy S, Bonanno JB, Burley SK, Swaminathan S. PMID: 16777962; PMCID: PMC1502539.
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    209. Crystal structures of two putative phosphoheptose isomerases. Proteins. 2006 Jun 01; 63(4):1092-6. Seetharaman J, Rajashankar KR, Solorzano V, Kniewel R, Lima CD, Bonanno JB, Burley SK, Swaminathan S. PMID: 16477602; PMCID: PMC1769519.
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    210. Crystal structure of a putative HTH-type transcriptional regulator yxaF from Bacillus subtilis. Proteins. 2006 Jun 01; 63(4):1087-91. Seetharaman J, Kumaran D, Bonanno JB, Burley SK, Swaminathan S. PMID: 16475182; PMCID: PMC1752215.
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    211. 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. Bellsolell L, Cho-Park PF, Poulin F, Sonenberg N, Burley SK. PMID: 16698552.
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    212. Cancer and kinases: reports from the front line. Genome Biol. 2006; 7(4):314. Burley SK. PMID: 16677415; PMCID: PMC1557988.
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    213. 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. Agarwal R, Bonanno JB, Burley SK, Swaminathan S. PMID: 16552139; PMCID: PMC1431508.
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    214. 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. Burley SK, Park F. PMID: 15998459; PMCID: PMC1175982.
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    215. 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. Padyana AK, Qiu H, Roll-Mecak A, Hinnebusch AG, Burley SK. PMID: 15964839.
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    216. 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. Matte A, Louie GV, Sivaraman J, Cygler M, Burley SK. PMID: 16511038; PMCID: PMC1952432.
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    218. X-ray structure of a Rex-family repressor/NADH complex insights into the mechanism of redox sensing. Structure. 2005 Jan; 13(1):43-54. Sickmier EA, Brekasis D, Paranawithana S, Bonanno JB, Paget MS, Burley SK, Kielkopf CL. PMID: 15642260.
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    219. High-throughput limited proteolysis/mass spectrometry for protein domain elucidation. J Struct Funct Genomics. 2005; 6(2-3):129-34. Gao X, Bain K, Bonanno JB, Buchanan M, Henderson D, Lorimer D, Marsh C, Reynes JA, Sauder JM, Schwinn K, Thai C, Burley SK. PMID: 16211509.
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    220. She2p is a novel RNA binding protein with a basic helical hairpin motif. Cell. 2004 Nov 12; 119(4):491-502. Niessing D, Hüttelmaier S, Zenklusen D, Singer RH, Burley SK. PMID: 15537539.
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    221. 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. 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 SK, Buchanan SG. PMID: 15507431.
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    222. X-ray structure of translation initiation factor eIF2gamma: implications for tRNA and eIF2alpha binding. J Biol Chem. 2004 Mar 12; 279(11):10634-42. Roll-Mecak A, Alone P, Cao C, Dever TE, Burley SK. PMID: 14688270.
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    223. Structure of nucleotide-binding domain 1 of the cystic fibrosis transmembrane conductance regulator. EMBO J. 2004 Jan 28; 23(2):282-93. Lewis HA, Buchanan SG, Burley SK, 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. PMID: 14685259; PMCID: PMC1271750.
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    224. Structural bases for CRMP function in plexin-dependent semaphorin3A signaling. EMBO J. 2004 Jan 14; 23(1):9-22. Deo RC, Schmidt EF, Elhabazi A, Togashi H, Burley SK, Strittmatter SM. PMID: 14685275; PMCID: PMC1271659.
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    225. Crystal structure of shikimate 5-dehydrogenase (SDH) bound to NADP: insights into function and evolution. Structure. 2003 Aug; 11(8):1005-13. Padyana AK, Burley SK. PMID: 12906831.
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    226. Crystal structure of the MazE/MazF complex: molecular bases of antidote-toxin recognition. Mol Cell. 2003 Apr; 11(4):875-84. Kamada K, Hanaoka F, Burley SK. PMID: 12718874.
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    227. A modular cross-linking approach for exploring protein interactions. J Am Chem Soc. 2003 Mar 05; 125(9):2416-25. Trester-Zedlitz M, Kamada K, Burley SK, Fenyö D, Chait BT, Muir TW. PMID: 12603129.
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    228. 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. Kamada K, Roeder RG, Burley SK. PMID: 12591941; PMCID: PMC151334.
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    229. 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. Nair SK, Burley SK. PMID: 12553908.
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    230. 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. Zuberek J, Wyslouch-Cieszynska A, Niedzwiecka A, Dadlez M, Stepinski J, Augustyniak W, Gingras AC, Zhang Z, Burley SK, Sonenberg N, Stolarski R, Darzynkiewicz E. PMID: 12554876; PMCID: PMC1370370.
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    231. Structural genomics. Methods Biochem Anal. 2003; 44:591-612. Burley SK, Bonanno JB. PMID: 12647406.
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    232. 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. Ray SS, Bonanno JB, Chen H, de Lencastre H, Wu S, Tomasz A, Burley SK. PMID: 12471609.
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    233. Uncoupling of initiation factor eIF5B/IF2 GTPase and translational activities by mutations that lower ribosome affinity. Cell. 2002 Dec 27; 111(7):1015-25. Shin BS, Maag D, Roll-Mecak A, Arefin MS, Burley SK, Lorsch JR, Dever TE. PMID: 12507428.
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    234. The kinetic mechanism of phosphomevalonate kinase. J Biol Chem. 2003 Feb 14; 278(7):4510-5. Pilloff D, Dabovic K, Romanowski MJ, Bonanno JB, Doherty M, Burley SK, Leyh TS. PMID: 12424232.
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    235. Cocrystal structures of diaminopimelate decarboxylase: mechanism, evolution, and inhibition of an antibiotic resistance accessory factor. Structure. 2002 Nov; 10(11):1499-508. Ray SS, Bonanno JB, Rajashankar KR, Pinho MG, He G, De Lencastre H, Tomasz A, Burley SK. PMID: 12429091.
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    236. X-ray structures of threonine aldolase complexes: structural basis of substrate recognition. Biochemistry. 2002 Oct 01; 41(39):11711-20. Kielkopf CL, Burley SK. PMID: 12269813.
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    237. X-ray structure of Saccharomyces cerevisiae homologous mitochondrial matrix factor 1 (Hmf1). Proteins. 2002 Aug 01; 48(2):431-6. Deaconescu AM, Roll-Mecak A, Bonanno JB, Gerchman SE, Kycia H, Studier FW, Burley SK. PMID: 12112709.
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    238. 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. Niedzwiecka A, Marcotrigiano J, Stepinski J, Jankowska-Anyszka M, Wyslouch-Cieszynska A, Dadlez M, Gingras AC, Mak P, Darzynkiewicz E, Sonenberg N, Burley SK, Stolarski R. PMID: 12054859.
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    239. Crystal structure of the Escherichia coli glucose-inhibited division protein B (GidB) reveals a methyltransferase fold. Proteins. 2002 Jun 01; 47(4):563-7. Romanowski MJ, Bonanno JB, Burley SK. PMID: 12001236.
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    240. Crystal structure of the Streptococcus pneumoniae phosphomevalonate kinase, a member of the GHMP kinase superfamily. Proteins. 2002 Jun 01; 47(4):568-71. Romanowski MJ, Bonanno JB, Burley SK. PMID: 12001237.
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    241. Crystal structure of the Escherichia coli shikimate kinase I (AroK) that confers sensitivity to mecillinam. Proteins. 2002 Jun 01; 47(4):558-62. Romanowski MJ, Burley SK. PMID: 12001235.
      View in: PubMed   Mentions: 10     Fields:    Translation:Cells
    242. Recognition of eIF4G by rotavirus NSP3 reveals a basis for mRNA circularization. Mol Cell. 2002 Jun; 9(6):1273-83. Groft CM, Burley SK. PMID: 12086624.
      View in: PubMed   Mentions: 66     Fields:    Translation:HumansAnimalsCells
    243. Structural genomics of proteins from conserved biochemical pathways and processes. Curr Opin Struct Biol. 2002 Jun; 12(3):383-91. Burley SK, Bonanno JB. PMID: 12127459.
      View in: PubMed   Mentions: 13     Fields:    Translation:Humans
    244. 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. Romanowski MJ, Gibney SA, Burley SK. PMID: 11948793.
      View in: PubMed   Mentions: 10     Fields:    Translation:Cells
    245. 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. Soccio RE, Adams RM, Romanowski MJ, Sehayek E, Burley SK, Breslow JL. PMID: 12011452; PMCID: PMC124508.
      View in: PubMed   Mentions: 73     Fields:    Translation:HumansAnimalsCells
    246. 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. Romanowski MJ, Soccio RE, Breslow JL, Burley SK. PMID: 12011453; PMCID: PMC124509.
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    247. Structuring the universe of proteins. Annu Rev Genomics Hum Genet. 2002; 3:243-62. Burley SK, Bonanno JB. PMID: 12194989.
      View in: PubMed   Mentions: 17     Fields:    Translation:HumansAnimalsCells
    248. Transcription factor complexes. Curr Opin Struct Biol. 2002 Apr; 12(2):225-30. Burley SK, Kamada K. PMID: 11959501.
      View in: PubMed   Mentions: 13     Fields:    Translation:HumansCells
    249. Structural genomics: a pipeline for providing structures for the biologist. Protein Sci. 2002 Apr; 11(4):723-38. Chance MR, Bresnick AR, Burley SK, 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. PMID: 11910018; PMCID: PMC2373525.
      View in: PubMed   Mentions: 57     Fields:    Translation:HumansAnimalsCells
    250. X-ray crystallographic studies of serotonin N-acetyltransferase catalysis and inhibition. J Mol Biol. 2002 Mar 22; 317(2):215-24. Wolf E, De Angelis J, Khalil EM, Cole PA, Burley SK. PMID: 11902838.
      View in: PubMed   Mentions: 25     Fields:    Translation:Cells
    251. Investigation of the roles of catalytic residues in serotonin N-acetyltransferase. J Biol Chem. 2002 May 17; 277(20):18118-26. Scheibner KA, De Angelis J, Burley SK, Cole PA. PMID: 11884405.
      View in: PubMed   Mentions: 31     Fields:    Translation:Cells
    252. Recognition of the rotavirus mRNA 3' consensus by an asymmetric NSP3 homodimer. Cell. 2002 Jan 11; 108(1):71-81. Deo RC, Groft CM, Rajashankar KR, Burley SK. PMID: 11792322.
      View in: PubMed   Mentions: 45     Fields:    Translation:HumansCells
    253. Structural biology of eIF4F: mRNA recognition and preparation in eukaryotic translation initiation. Adv Protein Chem. 2002; 61:269-97. Marcotrigiano J, Burley SK. PMID: 12461826.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansAnimalsCells
    254. [10] Dynamic light scattering in evaluating crystallizability of macromolecules. Methods Enzymol. 1997; 276:157-166. Ferré-D'Amaré AR, Burley SK. PMID: 27799091.
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