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Page 1
Biochemical and structural analyses reveal that the tumor suppressor neurofibromin (NF1) forms a high-affinity dimer.
Sherekar M, Han SW, Ghirlando R, Messing S, Drew M, Rabara D, Waybright T, Juneja P, O'Neill H, Stanley CB, Bhowmik D, Ramanathan A, Subramaniam S, Nissley DV, Gillette W, McCormick F, Esposito D. Sherekar M, et al. Among authors: ramanathan a. J Biol Chem. 2020 Jan 24;295(4):1105-1119. doi: 10.1074/jbc.RA119.010934. Epub 2019 Dec 13. J Biol Chem. 2020. PMID: 31836666 Free PMC article.
Folding propensity of intrinsically disordered proteins by osmotic stress.
Mansouri AL, Grese LN, Rowe EL, Pino JC, Chennubhotla SC, Ramanathan A, O'Neill HM, Berthelier V, Stanley CB. Mansouri AL, et al. Among authors: ramanathan a. Mol Biosyst. 2016 Nov 15;12(12):3695-3701. doi: 10.1039/c6mb00512h. Mol Biosyst. 2016. PMID: 27752679 Free PMC article.
Deep clustering of protein folding simulations.
Bhowmik D, Gao S, Young MT, Ramanathan A. Bhowmik D, et al. Among authors: ramanathan a. BMC Bioinformatics. 2018 Dec 21;19(Suppl 18):484. doi: 10.1186/s12859-018-2507-5. BMC Bioinformatics. 2018. PMID: 30577777 Free PMC article.
Uncovering a membrane-distal conformation of KRAS available to recruit RAF to the plasma membrane.
Van QN, López CA, Tonelli M, Taylor T, Niu B, Stanley CB, Bhowmik D, Tran TH, Frank PH, Messing S, Alexander P, Scott D, Ye X, Drew M, Chertov O, Lösche M, Ramanathan A, Gross ML, Hengartner NW, Westler WM, Markley JL, Simanshu DK, Nissley DV, Gillette WK, Esposito D, McCormick F, Gnanakaran S, Heinrich F, Stephen AG. Van QN, et al. Among authors: ramanathan a. Proc Natl Acad Sci U S A. 2020 Sep 29;117(39):24258-24268. doi: 10.1073/pnas.2006504117. Epub 2020 Sep 10. Proc Natl Acad Sci U S A. 2020. PMID: 32913056 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: ramanathan a. 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.
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: ramanathan a. 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.
Mechanism of glucocerebrosidase activation and dysfunction in Gaucher disease unraveled by molecular dynamics and deep learning.
Romero R, Ramanathan A, Yuen T, Bhowmik D, Mathew M, Munshi LB, Javaid S, Bloch M, Lizneva D, Rahimova A, Khan A, Taneja C, Kim SM, Sun L, New MI, Haider S, Zaidi M. Romero R, et al. Among authors: ramanathan a. Proc Natl Acad Sci U S A. 2019 Mar 12;116(11):5086-5095. doi: 10.1073/pnas.1818411116. Epub 2019 Feb 26. Proc Natl Acad Sci U S A. 2019. PMID: 30808805 Free PMC article.
Dynamic Profiling of β-Coronavirus 3CL Mpro Protease Ligand-Binding Sites.
Cho E, Rosa M, Anjum R, Mehmood S, Soban M, Mujtaba M, Bux K, Moin ST, Tanweer M, Dantu S, Pandini A, Yin J, Ma H, Ramanathan A, Islam B, Mey ASJS, Bhowmik D, Haider S. Cho E, et al. Among authors: ramanathan a. J Chem Inf Model. 2021 Jun 28;61(6):3058-3073. doi: 10.1021/acs.jcim.1c00449. Epub 2021 Jun 14. J Chem Inf Model. 2021. PMID: 34124899
448 results