Carlos Simmerling

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Asim OkurPostdoctoral Research Fellow, National Institutes of HealthVerified email at nhlbi.nih.gov
Thomas E. Cheatham, IIIProfessor of Medicinal Chemistry; Director Research Computing; University of UtahVerified email at utah.edu
Lauren WickstromCUNYVerified email at bmcc.cuny.edu
David A CaseRutgers UniversityVerified email at biomaps.rutgers.edu
Kenneth M. Merz Jr.University Distinguished Professor and Joseph Zichis Chair in Chemistry, Michigan State UniversityVerified email at msu.edu
Ray LuoMolecular Biology and Biochemistry, Biomedical Engineering, and Chemical and BiomolecularVerified email at uci.edu
koushik kasavajhalaSenior Scientist I, Schrödinger GmbHVerified email at schrodinger.com
Adrian RoitbergUniversity of Florida, Chemistry DepartmentVerified email at ufl.edu
Peter TongeStony Brook UniversityVerified email at stonybrook.edu
Arthur P. GrollmanProfessor of Pharmacological Sciences, Stony Brook UniversityVerified email at stonybrook.edu
Daniel R. RoeLaboratory of Computational Biology, NHLBI, NIHVerified email at nih.gov
Alexey OnufrievVirginia TechVerified email at vt.edu
Christina BergonzoResearch Chemist, NIST/IBBRVerified email at nist.gov
Kun SongAstraZenecaVerified email at astrazeneca.com
Ron ElberU of Texas at Austin, Dept of Chem and the Inst for Comput Eng and SciVerified email at ices.utexas.edu
Daniel RaleighVerified email at stonybrook.edu
Hai NguyenSchrödinger, IncVerified email at schrodinger.com
Robert C. RizzoProfessor, Stony Brook UniversityVerified email at stonybrook.edu
Xiaolin ChengThe Ohio State UniversityVerified email at osu.edu
Iwao OjimaDistinguished Professor of Chemistry, Director of ICB&DD, Stony Brook UniversityVerified email at stonybrook.edu

Carlos Simmerling

Marsha Laufer Chair in Physical & Quantitative Biology, SUNY Stony Brook

Verified email at stonybrook.edu - Homepage

Computational Biophysics


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The Amber biomolecular simulation programs DA Case, TE Cheatham III, T Darden, H Gohlke, R Luo, KM Merz Jr, ... Journal of computational chemistry 26 (16), 1668-1688, 2005	8994	2005
Comparison of multiple Amber force fields and development of improved protein backbone parameters V Hornak, R Abel, A Okur, B Strockbine, A Roitberg, C Simmerling Proteins: Structure, Function, and Bioinformatics 65 (3), 712-725, 2006	6679	2006
ff14SB: improving the accuracy of protein side chain and backbone parameters from ff99SB JA Maier, C Martinez, K Kasavajhala, L Wickstrom, KE Hauser, ... Journal of chemical theory and computation 11 (8), 3696-3713, 2015	6407	2015
Amber 14 DA Case, V Babin, J Berryman, RM Betz, Q Cai, DS Cerutti, ... University of California, 2014	4739*	2014
AMBER 9 DA Case, TA Darden, TE Cheatham III, CL Simmerling, J Wang, RE Duke, ... University of California, San Francisco 45, 2006	3835	2006
Amber 11 DA Case, TA Darden, TE Cheatham, CL Simmerling, J Wang, RE Duke, ... University of California, 2010	3683	2010
AMBER 2015 DA Case, J Berryman, RM Betz, DS Cerutti, TE Cheatham Iii, TA Darden, ... University of California, 2015	3301	2015
All-atom structure prediction and folding simulations of a stable protein C Simmerling, B Strockbine, AE Roitberg Journal of the American Chemical Society 124 (38), 11258-11259, 2002	704	2002
Amber 2021 DA Case, HM Aktulga, K Belfon, I Ben-Shalom, SR Brozell, DS Cerutti, ... University of California, San Francisco, 2021	614	2021
Amber 10 DA Case, TA Darden, TE Cheatham, CL Simmerling, J Wang, RE Duke, ... University of California, 2008	505*	2008
AMBER 8, University of California, San Francisco DA Case, TA Darden, TE Cheatham, CL Simmerling, J Wang, RE Duke, ... There is no corresponding record for this reference, 2004	459*	2004
ff19SB: Amino-acid-specific protein backbone parameters trained against quantum mechanics energy surfaces in solution C Tian, K Kasavajhala, KAA Belfon, L Raguette, H Huang, AN Migues, ... Journal of chemical theory and computation 16 (1), 528-552, 2019	438	2019
HIV-1 protease flaps spontaneously open and reclose in molecular dynamics simulations V Hornak, A Okur, RC Rizzo, C Simmerling Proceedings of the National Academy of Sciences 103 (4), 915-920, 2006	420	2006
Generalized Born model with a simple, robust molecular volume correction J Mongan, C Simmerling, JA McCammon, DA Case, A Onufriev Journal of chemical theory and computation 3 (1), 156-169, 2007	378	2007
Improved generalized born solvent model parameters for protein simulations H Nguyen, DR Roe, C Simmerling Journal of chemical theory and computation 9 (4), 2020-2034, 2013	348	2013
Amber 2015 (University of California, San Francisco) DA Case, IY Ben-Shalom, SR Brozell, DS Cerutti, TE Cheatham III, ... Available from ambermd. org/doc12/Amber15. pdf, 2015	281	2015
Three-dimensional molecular theory of solvation coupled with molecular dynamics in Amber T Luchko, S Gusarov, DR Roe, C Simmerling, DA Case, J Tuszynski, ... Journal of chemical theory and computation 6 (3), 607-624, 2010	265	2010
Evaluating the performance of the ff99SB force field based on NMR scalar coupling data L Wickstrom, A Okur, C Simmerling Biophysical journal 97 (3), 853-856, 2009	250	2009
AMBER 14; University of California: San Francisco, 2014 DA Case, V Babin, JT Berryman, RM Betz, Q Cai, DS Cerutti, ... Google Scholar There is no corresponding record for this reference, 1-826, 2014	226	2014
MOIL: A program for simulations of macromolecules R Elber, A Roitberg, C Simmerling, R Goldstein, H Li, G Verkhivker, ... Computer Physics Communications 91 (1-3), 159-189, 1995	202	1995

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