Carlos Simmerling

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Thomas E. Cheatham, IIIProfessor of Medicinal Chemistry; Director Research Computing; University of UtahVerified email at utah.edu
Asim OkurScientific Information Officer, National Institute of Mental Health, NIHVerified email at nih.gov
Kenneth M. Merz Jr.Staff, Lerner Research Institute; Professor, Michigan State UniversityVerified email at msu.edu
Lauren WickstromCUNYVerified email at bmcc.cuny.edu
Ray LuoMolecular Biology and Biochemistry, Biomedical Engineering, and Chemical and BiomolecularVerified email at uci.edu
David A CaseRutgers UniversityVerified email at biomaps.rutgers.edu
koushik kasavajhalaSenior Scientist II, SchrödingerVerified email at schrodinger.com
Adrian RoitbergFrank Harris Professor. Department of Chemistry. University of Florida.Verified 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
Ross C WalkerVerified email at sdsc.edu
Hai NguyenSchrödinger, IncVerified email at schrodinger.com
Ron ElberU of Texas at Austin, The Inst for Comput Eng and Sci, and MiTOMED PHARMA, Inc.Verified email at ices.utexas.edu
Daniel RaleighVerified email at stonybrook.edu
Robert C. RizzoProfessor, Stony Brook UniversityVerified email at stonybrook.edu
Xiaolin ChengProfessor, The Ohio State UniversityVerified email at osu.edu

Carlos Simmerling

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

Verified email at stonybrook.edu - Homepage

Computational Biophysics


Title Sort by citations Sort by year Sort by title	Cited by Cited by	Year
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	10562	2005
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	9501	2015
Amber 11 DA Case, TA Darden, TE Cheatham, CL Simmerling, J Wang, RE Duke, ... University of California, 2010	8650	2010
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	7574	2006
Amber 2021 DA Case, HM Aktulga, K Belfon, I Ben-Shalom, SR Brozell, DS Cerutti, ... University of California, San Francisco, 2021	5788	2021
AMBER 9 DA Case, TA Darden, TE Cheatham III, CL Simmerling, J Wang, RE Duke, ... University of California, San Francisco 45, 2006	3681	2006
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	1383	2019
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	725	2002
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	615*	2004
Amber 10 DA Case, TA Darden, TE Cheatham, CL Simmerling, J Wang, RE Duke, ... University of California, 2008	536*	2008
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	503	2013
AmberTools DA Case, HM Aktulga, K Belfon, DS Cerutti, GA Cisneros, VWD Cruzeiro, ... Journal of chemical information and modeling 63 (20), 6183-6191, 2023	460	2023
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	455	2007
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	448	2006
Amber 14 DA Case, V Babin, J Berryman, RM Betz, Q Cai, DS Cerutti, ... University of California, 2014	354*	2014
AMBER 5.0 DA Case, DA Pearlman, JW Caldwell, TE Cheatham III, WS Ross, ... University of California, San Francisco, 1997	352	1997
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	295	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	262	2009
Folding simulations for proteins with diverse topologies are accessible in days with a physics-based force field and implicit solvent H Nguyen, J Maier, H Huang, V Perrone, C Simmerling Journal of the American Chemical Society 136 (40), 13959-13962, 2014	252	2014
AMBER 14; University of California: San Francisco, 2014 DA Case, V Babin, JT Berryman, RM Betz, Q Cai, DS Cerutti, ... There is no corresponding record for this reference, 1-826, 2014	248	2014

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