Carlos Simmerling
Affiliations: | Chemistry | Stony Brook University, Stony Brook, NY, United States |
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"Carlos Simmerling"Mean distance: 3317.75
Children
Sign in to add trainee| Guanglei Cui | grad student | 2003 | SUNY Stony Brook |
| Xiaolin Cheng | grad student | 2004 | SUNY Stony Brook |
| Bentley Strockbine | grad student | 2005 | SUNY Stony Brook |
| Asim Okur | grad student | 2007 | SUNY Stony Brook |
| Daniel R. Roe | grad student | 2001-2007 | SUNY Stony Brook |
| Lauren Wickstrom | grad student | 2009 | SUNY Stony Brook |
| Fang Y. Ding | grad student | 2010 | SUNY Stony Brook |
| Arthur J. Campbell | grad student | 2011 | SUNY Stony Brook |
| Christina Bergonzo | grad student | 2012 | SUNY Stony Brook |
| Amber Carr | grad student | 2013 | SUNY Stony Brook |
| Yi Shang | grad student | 2013 | SUNY Stony Brook |
| Carmenza Martinez | grad student | 2014 | SUNY Stony Brook |
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Publications
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| Chen L, Roe DR, Kochert M, et al. (2024) k-Means NANI: an improved clustering algorithm for Molecular Dynamics simulations. Biorxiv : the Preprint Server For Biology |
| Cao X, Hummel MH, Wang Y, et al. (2024) Exact analytical algorithm for solvent accessible surface area and derivatives in implicit solvent molecular simulations on GPUs. Arxiv |
| Case DA, Aktulga HM, Belfon K, et al. (2023) AmberTools. Journal of Chemical Information and Modeling. 63: 6183-6191 |
| Kasavajhala K, Simmerling C. (2023) Exploring the Transferability of Replica Exchange Structure Reservoirs to Accelerate Generation of Ensembles for Alternate Hamiltonians or Protein Mutations. Journal of Chemical Theory and Computation. 19: 1931-1944 |
| Nikolić M, Brudar S, Coutsias E, et al. (2022) BioMThermDB 1.0: Thermophysical Database of Proteins in Solutions. International Journal of Molecular Sciences. 23 |
| Zou J, Li Z, Liu S, et al. (2021) Scaffold Hopping Transformations Using Auxiliary Restraints for Calculating Accurate Relative Binding Free Energies. Journal of Chemical Theory and Computation |
| Tian C, Kasavajhala K, Belfon KAA, et al. (2019) ff19SB: Amino-acid specific protein backbone parameters trained against quantum mechanics energy surfaces in solution. Journal of Chemical Theory and Computation |
| Zou J, Simmerling C, Raleigh DP. (2019) Dissecting the Energetics of Intrinsically Disordered Proteins via a Hybrid Experimental and Computational Approach. The Journal of Physical Chemistry. B |
| Zou J, Tian C, Simmerling C. (2019) Blinded prediction of protein-ligand binding affinity using Amber thermodynamic integration for the 2018 D3R grand challenge 4. Journal of Computer-Aided Molecular Design |
| Ghoreishi D, Cerutti DS, Fallon Z, et al. (2019) A Fast Implementation of the Nudged Elastic Band Method in AMBER. Journal of Chemical Theory and Computation |