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Discovery of Small-Molecule Inhibitors of SARS-CoV-2 Proteins Using a Computational and Experimental Pipeline.
Lau EY, Negrete OA, Bennett WFD, Bennion BJ, Borucki M, Bourguet F, Epstein A, Franco M, Harmon B, He S, Jones D, Kim H, Kirshner D, Lao V, Lo J, McLoughlin K, Mosesso R, Murugesh DK, Saada EA, Segelke B, Stefan MA, Stevenson GA, Torres MW, Weilhammer DR, Wong S, Yang Y, Zemla A, Zhang X, Zhu F, Allen JE, Lightstone FC. Lau EY, et al. Among authors: yang y. Front Mol Biosci. 2021 Jul 9;8:678701. doi: 10.3389/fmolb.2021.678701. eCollection 2021. Front Mol Biosci. 2021. PMID: 34327214 Free PMC article.
Membrane interactions of the globular domain and the hypervariable region of KRAS4b define its unique diffusion behavior.
Goswami D, Chen D, Yang Y, Gudla PR, Columbus J, Worthy K, Rigby M, Wheeler M, Mukhopadhyay S, Powell K, Burgan W, Wall V, Esposito D, Simanshu DK, Lightstone FC, Nissley DV, McCormick F, Turbyville T. Goswami D, et al. Among authors: yang y. Elife. 2020 Jan 20;9:e47654. doi: 10.7554/eLife.47654. Elife. 2020. PMID: 31958057 Free PMC article.
Machine learning-driven multiscale modeling reveals lipid-dependent dynamics of RAS signaling proteins.
Ingólfsson HI, Neale C, Carpenter TS, Shrestha R, López CA, Tran TH, Oppelstrup T, Bhatia H, Stanton LG, Zhang X, Sundram S, Di Natale F, Agarwal A, Dharuman G, Kokkila Schumacher SIL, Turbyville T, Gulten G, Van QN, Goswami D, Jean-Francois F, Agamasu C, Chen D, Hettige JJ, Travers T, Sarkar S, Surh MP, Yang Y, Moody A, Liu S, Van Essen BC, Voter AF, Ramanathan A, Hengartner NW, Simanshu DK, Stephen AG, Bremer PT, Gnanakaran S, Glosli JN, Lightstone FC, McCormick F, Nissley DV, Streitz FH. Ingólfsson HI, et al. Among authors: yang y. Proc Natl Acad Sci U S A. 2022 Jan 4;119(1):e2113297119. doi: 10.1073/pnas.2113297119. Proc Natl Acad Sci U S A. 2022. PMID: 34983849 Free PMC article.
Accelerators for Classical Molecular Dynamics Simulations of Biomolecules.
Jones D, Allen JE, Yang Y, Drew Bennett WF, Gokhale M, Moshiri N, Rosing TS. Jones D, et al. Among authors: yang y. J Chem Theory Comput. 2022 Jul 12;18(7):4047-4069. doi: 10.1021/acs.jctc.1c01214. Epub 2022 Jun 16. J Chem Theory Comput. 2022. PMID: 35710099 Free PMC article. Review.
Clustering Protein Binding Pockets and Identifying Potential Drug Interactions: A Novel Ligand-Based Featurization Method.
Stevenson GA, Kirshner D, Bennion BJ, Yang Y, Zhang X, Zemla A, Torres MW, Epstein A, Jones D, Kim H, Bennett WFD, Wong SE, Allen JE, Lightstone FC. Stevenson GA, et al. Among authors: yang y. J Chem Inf Model. 2023 Nov 13;63(21):6655-6666. doi: 10.1021/acs.jcim.3c00722. Epub 2023 Oct 17. J Chem Inf Model. 2023. PMID: 37847557 Free PMC article.
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