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Direct Modulators of K-Ras-Membrane Interactions.
Morstein J, Shrestha R, Van QN, López CA, Arora N, Tonelli M, Liang H, Chen D, Zhou Y, Hancock JF, Stephen AG, Turbyville TJ, Shokat KM. Morstein J, et al. Among authors: chen d. ACS Chem Biol. 2023 Sep 15;18(9):2082-2093. doi: 10.1021/acschembio.3c00413. Epub 2023 Aug 14. ACS Chem Biol. 2023. PMID: 37579045 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: chen d. 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: chen d. 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.
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: chen d. 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.
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: chen d. 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
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: chen d. 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: chen d. 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.
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