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Page 1
Algorithms for protein design.
Gainza P, Nisonoff HM, Donald BR. Gainza P, et al. Curr Opin Struct Biol. 2016 Aug;39:16-26. doi: 10.1016/j.sbi.2016.03.006. Epub 2016 Apr 14. Curr Opin Struct Biol. 2016. PMID: 27086078 Free PMC article. Review.
OSPREY 3.0: Open-source protein redesign for you, with powerful new features.
Hallen MA, Martin JW, Ojewole A, Jou JD, Lowegard AU, Frenkel MS, Gainza P, Nisonoff HM, Mukund A, Wang S, Holt GT, Zhou D, Dowd E, Donald BR. Hallen MA, et al. J Comput Chem. 2018 Nov 15;39(30):2494-2507. doi: 10.1002/jcc.25522. Epub 2018 Oct 14. J Comput Chem. 2018. PMID: 30368845 Free PMC article.
RNA language models predict mutations that improve RNA function.
Shulgina Y, Trinidad MI, Langeberg CJ, Nisonoff H, Chithrananda S, Skopintsev P, Nissley AJ, Patel J, Boger RS, Shi H, Yoon PH, Doherty EE, Pande T, Iyer AM, Doudna JA, Cate JHD. Shulgina Y, et al. Among authors: nisonoff h. Nat Commun. 2024 Dec 5;15(1):10627. doi: 10.1038/s41467-024-54812-y. Nat Commun. 2024. PMID: 39638800 Free PMC article.
GENTANGLE: integrated computational design of gene entanglements.
Martí JM, Hsu C, Rochereau C, Xu C, Blazejewski T, Nisonoff H, Leonard SP, Kang-Yun CS, Chlebek J, Ricci DP, Park D, Wang H, Listgarten J, Jiao Y, Allen JE. Martí JM, et al. Among authors: nisonoff h. Bioinformatics. 2024 Jul 1;40(7):btae380. doi: 10.1093/bioinformatics/btae380. Bioinformatics. 2024. PMID: 38905502 Free PMC article.
16 results