| Force fields for protein simulations JW Ponder, DA Case Advances in protein chemistry 66, 27-85, 2003 | 2290 | 2003 |
| Tertiary templates for proteins: use of packing criteria in the enumeration of allowed sequences for different structural classes JW Ponder, FM Richards Journal of molecular biology 193 (4), 775-791, 1987 | 1993 | 1987 |
| Polarizable atomic multipole water model for molecular mechanics simulation P Ren, JW Ponder The Journal of Physical Chemistry B 107 (24), 5933-5947, 2003 | 1552 | 2003 |
| Current status of the AMOEBA polarizable force field JW Ponder, C Wu, P Ren, VS Pande, JD Chodera, MJ Schnieders, ... The journal of physical chemistry B 114 (8), 2549-2564, 2010 | 1304 | 2010 |
| An efficient newton‐like method for molecular mechanics energy minimization of large molecules JW Ponder, FM Richards Journal of computational chemistry 8 (7), 1016-1024, 1987 | 1069 | 1987 |
| TINKER: Software tools for molecular design JW Ponder Washington University School of Medicine, Saint Louis, MO 3, 2004 | 780 | 2004 |
| Consistent treatment of inter‐and intramolecular polarization in molecular mechanics calculations P Ren, JW Ponder Journal of computational chemistry 23 (16), 1497-1506, 2002 | 651 | 2002 |
| Polarizable atomic multipole-based AMOEBA force field for proteins Y Shi, Z Xia, J Zhang, R Best, C Wu, JW Ponder, P Ren Journal of chemical theory and computation 9 (9), 4046-4063, 2013 | 602 | 2013 |
| Ion solvation thermodynamics from simulation with a polarizable force field A Grossfield, P Ren, JW Ponder Journal of the American Chemical Society 125 (50), 15671-15682, 2003 | 598 | 2003 |
| Polarizable atomic multipole-based molecular mechanics for organic molecules P Ren, C Wu, JW Ponder Journal of chemical theory and computation 7 (10), 3143-3161, 2011 | 444 | 2011 |
| Tinker 8: software tools for molecular design JA Rackers, Z Wang, C Lu, ML Laury, L Lagardère, MJ Schnieders, ... Journal of chemical theory and computation 14 (10), 5273-5289, 2018 | 361 | 2018 |
| Systematic improvement of a classical molecular model of water LP Wang, T Head-Gordon, JW Ponder, P Ren, JD Chodera, PK Eastman, ... The Journal of Physical Chemistry B 117 (34), 9956-9972, 2013 | 330 | 2013 |
| Analysis and application of potential energy smoothing and search methods for global optimization RV Pappu, RK Hart, JW Ponder The Journal of Physical Chemistry B 102 (48), 9725-9742, 1998 | 308 | 1998 |
| Accurate modeling of the intramolecular electrostatic energy of proteins MJ Dudek, JW Ponder Journal of Computational Chemistry 16 (7), 791-816, 1995 | 281 | 1995 |
| Algorithms for calculating excluded volume and its derivatives as a function of molecular conformation and their use in energy minimization CE Kundrot, JW Ponder, FM Richards Journal of computational chemistry 12 (3), 402-409, 1991 | 253 | 1991 |
| Temperature and pressure dependence of the AMOEBA water model P Ren, JW Ponder The Journal of Physical Chemistry B 108 (35), 13427-13437, 2004 | 239 | 2004 |
| Light-activated rhodopsin induces structural binding motif in G protein α subunit OG Kisselev, J Kao, JW Ponder, YC Fann, N Gautam, GR Marshall Proceedings of the National Academy of Sciences 95 (8), 4270-4275, 1998 | 218 | 1998 |
| Revised parameters for the AMOEBA polarizable atomic multipole water model ML Laury, LP Wang, VS Pande, T Head-Gordon, JW Ponder The Journal of Physical Chemistry B 119 (29), 9423-9437, 2015 | 214 | 2015 |
| Definition of a metal-dependent/Li (+)-inhibited phosphomonoesterase protein family based upon a conserved three-dimensional core structure. JD York, JW Ponder, PW Majerus Proceedings of the National Academy of Sciences 92 (11), 5149-5153, 1995 | 214 | 1995 |
| TINKER, Software Tools for Molecular Design, Version 4.2 JW Ponder Washington University School of Medicine, St. Louis, 2004 | 180 | 2004 |
