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Page 1
Cyclic peptide structure prediction and design using AlphaFold.
Rettie SA, Campbell KV, Bera AK, Kang A, Kozlov S, De La Cruz J, Adebomi V, Zhou G, DiMaio F, Ovchinnikov S, Bhardwaj G. Rettie SA, et al. Among authors: ovchinnikov s. bioRxiv [Preprint]. 2023 Feb 26:2023.02.25.529956. doi: 10.1101/2023.02.25.529956. bioRxiv. 2023. PMID: 36865323 Free PMC article. Preprint.
A demonstration of unsupervised machine learning in species delimitation.
Derkarabetian S, Castillo S, Koo PK, Ovchinnikov S, Hedin M. Derkarabetian S, et al. Among authors: ovchinnikov s. Mol Phylogenet Evol. 2019 Oct;139:106562. doi: 10.1016/j.ympev.2019.106562. Epub 2019 Jul 16. Mol Phylogenet Evol. 2019. PMID: 31323334 Free PMC article.
Cryo-EM structure of the protein-conducting ERAD channel Hrd1 in complex with Hrd3.
Schoebel S, Mi W, Stein A, Ovchinnikov S, Pavlovicz R, DiMaio F, Baker D, Chambers MG, Su H, Li D, Rapoport TA, Liao M. Schoebel S, et al. Among authors: ovchinnikov s. Nature. 2017 Aug 17;548(7667):352-355. doi: 10.1038/nature23314. Epub 2017 Jul 6. Nature. 2017. PMID: 28682307 Free PMC article.
Protein structure prediction using Rosetta in CASP12.
Ovchinnikov S, Park H, Kim DE, DiMaio F, Baker D. Ovchinnikov S, et al. Proteins. 2018 Mar;86 Suppl 1(Suppl 1):113-121. doi: 10.1002/prot.25390. Epub 2017 Oct 8. Proteins. 2018. PMID: 28940798 Free PMC article.
Protein homology model refinement by large-scale energy optimization.
Park H, Ovchinnikov S, Kim DE, DiMaio F, Baker D. Park H, et al. Among authors: ovchinnikov s. Proc Natl Acad Sci U S A. 2018 Mar 20;115(12):3054-3059. doi: 10.1073/pnas.1719115115. Epub 2018 Mar 5. Proc Natl Acad Sci U S A. 2018. PMID: 29507254 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: ovchinnikov s. 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.
124 results