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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. Proteins. 2022 May;90(5):1054-1080. doi: 10.1002/prot.26250. Epub 2021 Oct 9. Proteins. 2022. PMID: 34580920 Free PMC article.
Computational design of nanomolar-binding antibodies specific to multiple SARS-CoV-2 variants by engineering a specificity switch of antibody 80R using RosettaAntibodyDesign (RAbD) results in potential generalizable therapeutic antibodies for novel SARS-CoV-2 virus.
Hernandez NE, Jankowski W, Frick R, Kelow SP, Lubin JH, Simhadri V, Adolf-Bryfogle J, Khare SD, Dunbrack RL Jr, Gray JJ, Sauna ZE. Hernandez NE, et al. Among authors: lubin jh. Heliyon. 2023 Apr;9(4):e15032. doi: 10.1016/j.heliyon.2023.e15032. Epub 2023 Apr 3. Heliyon. 2023. PMID: 37035348 Free PMC article.
Corrigendum to "Computational design of nanomolar-binding antibodies specific to multiple SARS-CoV-2 variants by engineering a specificity switch of antibody 80R using RosettaAntibodyDesign (RAbD) results in potential generalizable therapeutic antibodies for novel SARS-CoV-2 virus" [Heliyon 9(4) (April 2023) e15032].
Hernandez NE, Jankowski W, Frick R, Kelow SP, Lubin JH, Simhadri V, Adolf-Bryfogle J, Khare SD, Dunbrack RL Jr, Gray JJ, Sauna ZE. Hernandez NE, et al. Among authors: lubin jh. Heliyon. 2023 Jul 6;9(8):e17901. doi: 10.1016/j.heliyon.2023.e17901. eCollection 2023 Aug. Heliyon. 2023. PMID: 37701412 Free PMC article.
Genetic and Structural Analysis of SARS-CoV-2 Spike Protein for Universal Epitope Selection.
Markosian C, Staquicini DI, Dogra P, Dodero-Rojas E, Lubin JH, Tang FHF, Smith TL, Contessoto VG, Libutti SK, Wang Z, Cristini V, Khare SD, Whitford PC, Burley SK, Onuchic JN, Pasqualini R, Arap W. Markosian C, et al. Among authors: lubin jh. Mol Biol Evol. 2022 May 3;39(5):msac091. doi: 10.1093/molbev/msac091. Mol Biol Evol. 2022. PMID: 35511693 Free PMC article.
Macromolecular modeling and design in Rosetta: recent methods and frameworks.
Leman JK, Weitzner BD, Lewis SM, Adolf-Bryfogle J, Alam N, Alford RF, Aprahamian M, Baker D, Barlow KA, Barth P, Basanta B, Bender BJ, Blacklock K, Bonet J, Boyken SE, Bradley P, Bystroff C, Conway P, Cooper S, Correia BE, Coventry B, Das R, De Jong RM, DiMaio F, Dsilva L, Dunbrack R, Ford AS, Frenz B, Fu DY, Geniesse C, Goldschmidt L, Gowthaman R, Gray JJ, Gront D, Guffy S, Horowitz S, Huang PS, Huber T, Jacobs TM, Jeliazkov JR, Johnson DK, Kappel K, Karanicolas J, Khakzad H, Khar KR, Khare SD, Khatib F, Khramushin A, King IC, Kleffner R, Koepnick B, Kortemme T, Kuenze G, Kuhlman B, Kuroda D, Labonte JW, Lai JK, Lapidoth G, Leaver-Fay A, Lindert S, Linsky T, London N, Lubin JH, Lyskov S, Maguire J, Malmström L, Marcos E, Marcu O, Marze NA, Meiler J, Moretti R, Mulligan VK, Nerli S, Norn C, Ó'Conchúir S, Ollikainen N, Ovchinnikov S, Pacella MS, Pan X, Park H, Pavlovicz RE, Pethe M, Pierce BG, Pilla KB, Raveh B, Renfrew PD, Burman SSR, Rubenstein A, Sauer MF, Scheck A, Schief W, Schueler-Furman O, Sedan Y, Sevy AM, Sgourakis NG, Shi L, Siegel JB, Silva DA, Smith S, Song Y, Stein A, Szegedy M, Teets FD, Thyme SB, Wang RY, Watkins A, Zimmerman L, Bonneau R. Leman JK, et al. Among authors: lubin jh. Nat Methods. 2020 Jul;17(7):665-680. doi: 10.1038/s41592-020-0848-2. Epub 2020 Jun 1. Nat Methods. 2020. PMID: 32483333 Free PMC article. Review.
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. Among authors: lubin jh. 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.
[No title available]
[No authors listed] [No authors listed] PMID: 35560880
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. bioRxiv [Preprint]. 2020 Dec 7:2020.12.01.406637. doi: 10.1101/2020.12.01.406637. bioRxiv. 2020. PMID: 33299989 Free PMC article. Updated. Preprint.
262 results