| 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 | 8743 | 2015 |
| Amber 2021 DA Case, HM Aktulga, K Belfon, I Ben-Shalom, SR Brozell, DS Cerutti, ... University of California, San Francisco, 2021 | 5526 | 2021 |
| 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 | 1177 | 2019 |
| AmberTools DA Case, HM Aktulga, K Belfon, DS Cerutti, GA Cisneros, VWD Cruzeiro, ... Journal of chemical information and modeling 63 (20), 6183-6191, 2023 | 243 | 2023 |
| Role of urea–aromatic stacking interactions in stabilizing the aromatic residues of the protein in urea-induced denatured state S Goyal, A Chattopadhyay, K Kasavajhala, UD Priyakumar Journal of the American Chemical Society 139 (42), 14931-14946, 2017 | 62 | 2017 |
| Benchmarking refined and unrefined AlphaFold2 structures for hit discovery Y Zhang, M Vass, D Shi, E Abualrous, JM Chambers, N Chopra, C Higgs, ... Journal of Chemical Information and Modeling 63 (6), 1656-1667, 2023 | 54 | 2023 |
| AMBER 22 reference manual DA Case, RE Duke, RC Walker, NR Skrynnikov, TE Cheatham III, ... University of California, San Francisco, United States-California, 2022 | 36 | 2022 |
| Dispersion interactions between urea and nucleobases contribute to the destabilization of RNA by urea in aqueous solution K Kasavajhala, S Bikkina, I Patil, AD MacKerell Jr, UD Priyakumar The Journal of Physical Chemistry B 119 (9), 3755-3761, 2015 | 23 | 2015 |
| Exploring protocols to build reservoirs to accelerate temperature replica exchange MD simulations K Kasavajhala, K Lam, C Simmerling Journal of chemical theory and computation 16 (12), 7776-7799, 2020 | 13 | 2020 |
| Accelerating the ensemble convergence of RNA hairpin simulations with a replica exchange structure reservoir K Lam, K Kasavajhala, S Gunasekera, C Simmerling Journal of chemical theory and computation 18 (6), 3930-3947, 2022 | 10 | 2022 |
| Extracting representative structures from protein conformational ensembles A Perez, A Roy, K Kasavajhala, A Wagaman, KA Dill, JL MacCallum Proteins: Structure, Function, and Bioinformatics 82 (10), 2671-2680, 2014 | 7 | 2014 |
| Exploring the Transferability of Replica Exchange Structure Reservoirs to Accelerate Generation of Ensembles for Alternate Hamiltonians or Protein Mutations K Kasavajhala, C Simmerling Journal of chemical theory and computation 19 (6), 1931-1944, 2023 | 2 | 2023 |
| Using Structure Reservoirs to Accelerate Biomolecular Simulations K Kasavajhala State University of New York at Stony Brook, 2020 | | 2020 |
| Improving REMD efficiency with Monte Carlo moves using a structure reservoir K Kasavajhala, K Lam, C Simmerling ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY 258, 2019 | | 2019 |
| Urea-aromatic interactions: Protein unfolding to urea transporters S Goyal, A Chattopadhyay, K Kasavajhala, U Priyakumar ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY 256, 2018 | | 2018 |
| Improved generalized born water model for MD simulations of proteins and nucleic acids C Simmerling, H Nguyen, K Kasavajhala, H Huang, K Lam ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY 252, 2016 | | 2016 |
| Combining thermal, chemical, and mechanical perturbations to study protein folding: Molecular dynamics studies on Trp-cage miniprotein, and Titin I27 K Kasavajhala, N Bung, UD Priyakumar ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY 243, 2012 | | 2012 |
| ff14SB: Improving the accuracy of protein side chain and backbone parameters from ff99SB: Supporting Information J Maier, C Martinez, K Kasavajhala, L Wickstrom, K Hauser, C Simmerling | | |
| Exploring Protocols to build reservoirs to accelerate Replica Exchange MD simulations K Kasavajhala, K Lam, C Simmerling | | |
