| OPLS3: a force field providing broad coverage of drug-like small molecules and proteins E Harder, W Damm, J Maple, C Wu, M Reboul, JY Xiang, L Wang, ... Journal of chemical theory and computation 12 (1), 281-296, 2015 | 2750 | 2015 |
| Accurate and reliable prediction of relative ligand binding potency in prospective drug discovery by way of a modern free-energy calculation protocol and force field L Wang, Y Wu, Y Deng, B Kim, L Pierce, G Krilov, D Lupyan, S Robinson, ... Journal of the American Chemical Society 137 (7), 2695-2703, 2015 | 1092 | 2015 |
| Structural organization of bacterial RNA polymerase holoenzyme and the RNA polymerase-promoter open complex V Mekler, E Kortkhonjia, J Mukhopadhyay, J Knight, A Revyakin, ... Cell 108 (5), 599-614, 2002 | 349 | 2002 |
| Antibacterial peptide microcin J25 inhibits transcription by binding within and obstructing the RNA polymerase secondary channel J Mukhopadhyay, E Sineva, J Knight, RM Levy, RH Ebright Molecular cell 14 (6), 739-751, 2004 | 251 | 2004 |
| Opening and closing of the bacterial RNA polymerase clamp A Chakraborty, D Wang, YW Ebright, Y Korlann, E Kortkhonjia, T Kim, ... Science 337 (6094), 591-595, 2012 | 243 | 2012 |
| λ‐Dynamics free energy simulation methods JL Knight, CL Brooks III Journal of computational chemistry 30 (11), 1692-1700, 2009 | 205 | 2009 |
| Modeling local structural rearrangements using FEP/REST: application to relative binding affinity predictions of CDK2 inhibitors L Wang, Y Deng, JL Knight, Y Wu, B Kim, W Sherman, JC Shelley, T Lin, ... Journal of chemical theory and computation 9 (2), 1282-1293, 2013 | 204 | 2013 |
| MATCH: An atom‐typing toolset for molecular mechanics force fields JD Yesselman, DJ Price, JL Knight, CL Brooks III Journal of computational chemistry 33 (2), 189-202, 2012 | 176 | 2012 |
| HIV-1 reverse transcriptase structure with RNase H inhibitor dihydroxy benzoyl naphthyl hydrazone bound at a novel site DM Himmel, SG Sarafianos, S Dharmasena, MM Hossain, ... ACS chemical biology 1 (11), 702-712, 2006 | 169 | 2006 |
| Constant pH molecular dynamics simulations of nucleic acids in explicit solvent GB Goh, JL Knight, CL Brooks Journal of chemical theory and computation 8 (1), 36-46, 2011 | 99 | 2011 |
| Multisite λ dynamics for simulated structure–activity relationship studies JL Knight, CL Brooks III Journal of chemical theory and computation 7 (9), 2728-2739, 2011 | 95 | 2011 |
| On the mechanism of crystalline polymorph selection by polymer heteronuclei V López-Mejías, JL Knight, CL Brooks III, AJ Matzger Langmuir 27 (12), 7575-7579, 2011 | 85 | 2011 |
| Surveying implicit solvent models for estimating small molecule absolute hydration free energies JL Knight, CL Brooks III Journal of computational chemistry 32 (13), 2909-2923, 2011 | 80 | 2011 |
| pH-dependent dynamics of complex RNA macromolecules GB Goh, JL Knight, CL Brooks III Journal of chemical theory and computation 9 (2), 935-943, 2013 | 58 | 2013 |
| Applying efficient implicit nongeometric constraints in alchemical free energy simulations JL Knight, CL Brooks III Journal of computational chemistry 32 (16), 3423-3432, 2011 | 47 | 2011 |
| Distance-restrained docking of rifampicin and rifamycin SV to RNA polymerase using systematic FRET measurements: developing benchmarks of model quality and reliability JL Knight, V Mekler, J Mukhopadhyay, RH Ebright, RM Levy Biophysical journal 88 (2), 925-938, 2005 | 43 | 2005 |
| Assessing the quality of absolute hydration free energies among CHARMM‐compatible ligand parameterization schemes JL Knight, JD Yesselman, CL Brooks III Journal of computational chemistry 34 (11), 893-903, 2013 | 37 | 2013 |
| Toward accurate prediction of the protonation equilibrium of nucleic acids GB Goh, JL Knight, CL Brooks III The journal of physical chemistry letters 4 (5), 760-766, 2013 | 37 | 2013 |
| Exploring structural variability in X-ray crystallographic models using protein local optimization by torsion-angle sampling JL Knight, Z Zhou, E Gallicchio, DM Himmel, RA Friesner, E Arnold, ... Acta Crystallographica Section D: Biological Crystallography 64 (4), 383-396, 2008 | 28 | 2008 |
| Leveraging data fusion strategies in multireceptor lead optimization MM/GBSA End-point methods JL Knight, G Krilov, KW Borrelli, J Williams, JR Gunn, A Clowes, L Cheng, ... Journal of chemical theory and computation 10 (8), 3207-3220, 2014 | 26 | 2014 |
