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RCSB Protein Data bank: Tools for visualizing and understanding biological macromolecules in 3D.
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. Burley SK, et al. Among authors: craig pa. Protein Sci. 2022 Dec;31(12):e4482. doi: 10.1002/pro.4482. Protein Sci. 2022. PMID: 36281733 Free PMC article.
Virtual Boot Camp: COVID-19 evolution and structural biology.
Burley SK, Bromberg Y, Craig P, Duffy S, Dutta S, Hall BL, Hudson BP, Jiang J, D Khare S, Koeppe JR, Lubin JH, Mills SA, Pikaart MJ, Roberts R, Sarma V, Singh J, Tischfield JA, Xie L, Zardecki C. Burley SK, et al. Biochem Mol Biol Educ. 2020 Sep;48(5):511-513. doi: 10.1002/bmb.21428. Epub 2020 Aug 14. Biochem Mol Biol Educ. 2020. PMID: 32797732 Free PMC article. No abstract available.
Evolution of the SARS-CoV-2 proteome in three dimensions (3D) during the first 6 months of the COVID-19 pandemic.
Lubin JH, Zardecki C, Dolan EM, Lu C, Shen Z, Dutta S, Westbrook JD, Hudson BP, Goodsell DS, Williams JK, Voigt M, Sarma V, Xie L, Venkatachalam T, Arnold S, Alfaro Alvarado LH, Catalfano K, Khan A, McCarthy E, Staggers S, Tinsley B, Trudeau A, Singh J, Whitmore L, Zheng H, Benedek M, Currier J, Dresel M, Duvvuru A, Dyszel B, Fingar E, Hennen EM, Kirsch M, Khan AA, Labrie-Cleary C, Laporte S, Lenkeit E, Martin K, Orellana M, Ortiz-Alvarez de la Campa M, Paredes I, Wheeler B, Rupert A, Sam A, See K, Soto Zapata S, Craig PA, Hall BL, Jiang J, Koeppe JR, Mills SA, Pikaart MJ, Roberts R, Bromberg Y, Hoyer JS, Duffy S, Tischfield J, Ruiz FX, Arnold E, Baum J, Sandberg J, Brannigan G, Khare SD, Burley SK. Lubin JH, et al. Among authors: craig pa. Proteins. 2022 May;90(5):1054-1080. doi: 10.1002/prot.26250. Epub 2021 Oct 9. Proteins. 2022. PMID: 34580920 Free PMC article.
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.
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. Burley SK, et al. Among authors: craig pa. Nucleic Acids Res. 2023 Jan 6;51(D1):D488-D508. doi: 10.1093/nar/gkac1077. Nucleic Acids Res. 2023. PMID: 36420884 Free PMC article.
Updated resources for exploring experimentally-determined PDB structures and Computed Structure Models at the RCSB Protein Data Bank.
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. Burley SK, et al. Among authors: craig pa. Nucleic Acids Res. 2024 Nov 28:gkae1091. doi: 10.1093/nar/gkae1091. Online ahead of print. Nucleic Acids Res. 2024. PMID: 39607707
Annotation of proteins of unknown function: initial enzyme results.
McKay T, Hart K, Horn A, Kessler H, Dodge G, Bardhi K, Bardhi K, Mills JL, Bernstein HJ, Craig PA. McKay T, et al. Among authors: craig pa. J Struct Funct Genomics. 2015 Mar;16(1):43-54. doi: 10.1007/s10969-015-9194-5. Epub 2015 Jan 29. J Struct Funct Genomics. 2015. PMID: 25630330 Free PMC article.
Evolution of the SARS-CoV-2 proteome in three dimensions (3D) during the first six months of the COVID-19 pandemic.
Lubin JH, Zardecki C, Dolan EM, Lu C, Shen Z, Dutta S, Westbrook JD, Hudson BP, Goodsell DS, Williams JK, Voigt M, Sarma V, Xie L, Venkatachalam T, Arnold S, Alvarado LHA, Catalfano K, Khan A, McCarthy E, Staggers S, Tinsley B, Trudeau A, Singh J, Whitmore L, Zheng H, Benedek M, Currier J, Dresel M, Duvvuru A, Dyszel B, Fingar E, Hennen EM, Kirsch M, Khan AA, Labrie-Cleary C, Laporte S, Lenkeit E, Martin K, Orellana M, de la Campa MO, Paredes I, Wheeler B, Rupert A, Sam A, See K, Zapata SS, Craig PA, Hall BL, Jiang J, Koeppe JR, Mills SA, Pikaart MJ, Roberts R, Bromberg Y, Hoyer JS, Duffy S, Tischfield J, Ruiz FX, Arnold E, Baum J, Sandberg J, Brannigan G, Khare SD, Burley SK. Lubin JH, et al. Among authors: craig pa. bioRxiv [Preprint]. 2020 Dec 7:2020.12.01.406637. doi: 10.1101/2020.12.01.406637. bioRxiv. 2020. Update in: Proteins. 2022 May;90(5):1054-1080. doi: 10.1002/prot.26250 PMID: 33299989 Free PMC article. Updated. Preprint.
46 results