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AI Meets Exascale Computing: Advancing Cancer Research With Large-Scale High Performance Computing.
Bhattacharya T, Brettin T, Doroshow JH, Evrard YA, Greenspan EJ, Gryshuk AL, Hoang TT, Lauzon CBV, Nissley D, Penberthy L, Stahlberg E, Stevens R, Streitz F, Tourassi G, Xia F, Zaki G. Bhattacharya T, et al. Among authors: streitz f. Front Oncol. 2019 Oct 2;9:984. doi: 10.3389/fonc.2019.00984. eCollection 2019. Front Oncol. 2019. PMID: 31632915 Free PMC article. Review.
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: streitz fh. 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.
Asynchronous Reciprocal Coupling of Martini 2.2 Coarse-Grained and CHARMM36 All-Atom Simulations in an Automated Multiscale Framework.
López CA, Zhang X, Aydin F, Shrestha R, Van QN, Stanley CB, Carpenter TS, Nguyen K, Patel LA, Chen D, Burns V, Hengartner NW, Reddy TJE, Bhatia H, Di Natale F, Tran TH, Chan AH, Simanshu DK, Nissley DV, Streitz FH, Stephen AG, Turbyville TJ, Lightstone FC, Gnanakaran S, Ingólfsson HI, Neale C. López CA, et al. Among authors: streitz fh. J Chem Theory Comput. 2022 Aug 9;18(8):5025-5045. doi: 10.1021/acs.jctc.2c00168. Epub 2022 Jul 22. J Chem Theory Comput. 2022. PMID: 35866871
The confluence of machine learning and multiscale simulations.
Bhatia H, Aydin F, Carpenter TS, Lightstone FC, Bremer PT, Ingólfsson HI, Nissley DV, Streitz FH. Bhatia H, et al. Among authors: streitz fh. Curr Opin Struct Biol. 2023 Jun;80:102569. doi: 10.1016/j.sbi.2023.102569. Epub 2023 Mar 24. Curr Opin Struct Biol. 2023. PMID: 36966691 Review.
Machine Learning-Driven Multiscale Modeling: Bridging the Scales with a Next-Generation Simulation Infrastructure.
Ingólfsson HI, Bhatia H, Aydin F, Oppelstrup T, López CA, Stanton LG, Carpenter TS, Wong S, Di Natale F, Zhang X, Moon JY, Stanley CB, Chavez JR, Nguyen K, Dharuman G, Burns V, Shrestha R, Goswami D, Gulten G, Van QN, Ramanathan A, Van Essen B, Hengartner NW, Stephen AG, Turbyville T, Bremer PT, Gnanakaran S, Glosli JN, Lightstone FC, Nissley DV, Streitz FH. Ingólfsson HI, et al. Among authors: streitz fh. J Chem Theory Comput. 2023 May 9;19(9):2658-2675. doi: 10.1021/acs.jctc.2c01018. Epub 2023 Apr 19. J Chem Theory Comput. 2023. PMID: 37075065 Free PMC article.
Membrane lipids drive formation of KRAS4b-RAF1 RBDCRD nanoclusters on the membrane.
Shrestha R, Carpenter TS, Van QN, Agamasu C, Tonelli M, Aydin F, Chen D, Gulten G, Glosli JN, López CA, Oppelstrup T, Neale C, Gnanakaran S, Gillette WK, Ingólfsson HI, Lightstone FC, Stephen AG, Streitz FH, Nissley DV, Turbyville TJ. Shrestha R, et al. Among authors: streitz fh. Commun Biol. 2024 Feb 28;7(1):242. doi: 10.1038/s42003-024-05916-0. Commun Biol. 2024. PMID: 38418613 Free PMC article.
Author Correction: Membrane lipids drive formation of KRAS4b-RAF1 RBDCRD nanoclusters on the membrane.
Shrestha R, Carpenter TS, Van QN, Agamasu C, Tonelli M, Aydin F, Chen D, Gulten G, Glosli JN, López CA, Oppelstrup T, Neale C, Gnanakaran S, Gillette WK, Ingólfsson HI, Lightstone FC, Stephen AG, Streitz FH, Nissley DV, Turbyville TJ. Shrestha R, et al. Among authors: streitz fh. Commun Biol. 2024 Apr 11;7(1):445. doi: 10.1038/s42003-024-06061-4. Commun Biol. 2024. PMID: 38605143 Free PMC article. No abstract available.
Exploring CRD mobility during RAS/RAF engagement at the membrane.
Nguyen K, López CA, Neale C, Van QN, Carpenter TS, Di Natale F, Travers T, Tran TH, Chan AH, Bhatia H, Frank PH, Tonelli M, Zhang X, Gulten G, Reddy T, Burns V, Oppelstrup T, Hengartner N, Simanshu DK, Bremer PT, Chen D, Glosli JN, Shrestha R, Turbyville T, Streitz FH, Nissley DV, Ingólfsson HI, Stephen AG, Lightstone FC, Gnanakaran S. Nguyen K, et al. Among authors: streitz fh. Biophys J. 2022 Oct 4;121(19):3630-3650. doi: 10.1016/j.bpj.2022.06.035. Epub 2022 Jul 1. Biophys J. 2022. PMID: 35778842 Free PMC article.
Molecular dynamics simulations of temperature equilibration in dense hydrogen.
Glosli JN, Graziani FR, More RM, Murillo MS, Streitz FH, Surh MP, Benedict LX, Hau-Riege S, Langdon AB, London RA. Glosli JN, et al. Among authors: streitz fh. Phys Rev E Stat Nonlin Soft Matter Phys. 2008 Aug;78(2 Pt 2):025401. doi: 10.1103/PhysRevE.78.025401. Epub 2008 Aug 18. Phys Rev E Stat Nonlin Soft Matter Phys. 2008. PMID: 18850889 Free article.
22 results