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Computational design of soluble functional analogues of integral membrane proteins.
Goverde CA, Pacesa M, Goldbach N, Dornfeld LJ, Balbi PEM, Georgeon S, Rosset S, Kapoor S, Choudhury J, Dauparas J, Schellhaas C, Kozlov S, Baker D, Ovchinnikov S, Vecchio AJ, Correia BE. Goverde CA, et al. Among authors: ovchinnikov s. bioRxiv [Preprint]. 2024 Mar 7:2023.05.09.540044. doi: 10.1101/2023.05.09.540044. bioRxiv. 2024. Update in: Nature. 2024 Jul;631(8020):449-458. doi: 10.1038/s41586-024-07601-y PMID: 38496615 Free PMC article. Updated. Preprint.
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.
An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12.
Keasar C, McGuffin LJ, Wallner B, Chopra G, Adhikari B, Bhattacharya D, Blake L, Bortot LO, Cao R, Dhanasekaran BK, Dimas I, Faccioli RA, Faraggi E, Ganzynkowicz R, Ghosh S, Ghosh S, Giełdoń A, Golon L, He Y, Heo L, Hou J, Khan M, Khatib F, Khoury GA, Kieslich C, Kim DE, Krupa P, Lee GR, Li H, Li J, Lipska A, Liwo A, Maghrabi AHA, Mirdita M, Mirzaei S, Mozolewska MA, Onel M, Ovchinnikov S, Shah A, Shah U, Sidi T, Sieradzan AK, Ślusarz M, Ślusarz R, Smadbeck J, Tamamis P, Trieber N, Wirecki T, Yin Y, Zhang Y, Bacardit J, Baranowski M, Chapman N, Cooper S, Defelicibus A, Flatten J, Koepnick B, Popović Z, Zaborowski B, Baker D, Cheng J, Czaplewski C, Delbem ACB, Floudas C, Kloczkowski A, Ołdziej S, Levitt M, Scheraga H, Seok C, Söding J, Vishveshwara S, Xu D; Foldit Players consortium; Crivelli SN. Keasar C, et al. Among authors: ovchinnikov s. Sci Rep. 2018 Jul 2;8(1):9939. doi: 10.1038/s41598-018-26812-8. Sci Rep. 2018. PMID: 29967418 Free PMC article.
Accurate de novo design of high-affinity protein binding macrocycles using deep learning.
Rettie SA, Juergens D, Adebomi V, Bueso YF, Zhao Q, Leveille AN, Liu A, Bera AK, Wilms JA, Üffing A, Kang A, Brackenbrough E, Lamb M, Gerben SR, Murray A, Levine PM, Schneider M, Vasireddy V, Ovchinnikov S, Weiergräber OH, Willbold D, Kritzer JA, Mougous JD, Baker D, DiMaio F, Bhardwaj G. Rettie SA, et al. Among authors: ovchinnikov s. bioRxiv [Preprint]. 2024 Nov 18:2024.11.18.622547. doi: 10.1101/2024.11.18.622547. bioRxiv. 2024. PMID: 39605685 Free PMC article. Preprint.
124 results