Jay W. Ponder

Research in my group focuses on computational chemistry. In particular, we are involved in the development and application of computational tools addressing current problems in structural biology, protein engineering, physical organic chemistry and drug design. We write and distribute software packages ranging from macromolecular mechanics and dynamics simulation (Tinker & Tinker9), to empirical packing analysis of protein structure (ProPak), to sequence level analysis (Sleuth), and ab initio protein structure prediction (using DistGeom). Our current work centers on: (1) application of the AMOEBA polarizable atomic multipole force field, (2) development and validation of the next-generation HIPPO model, (3) accurate estimation of ligand binding free energies and other intermolecular interactions, and (4) efficient conformational search algorithms for multi-dimensional potential energy surfaces.

A New Method to Calculate Broadband Dielectric Spectra of Solvents from Molecular Dynamics Simulations Demonstrated with Polarizable Force Fields, R. A. Bone, M. K. J. Chung, J. W. Ponder, D. Riccardi, C. Muzny, R. Sundararaman and K. Schwarz, J. Chem. Phys., 161, 064306 (2024) [PMCID:PMC11324330] [PDF]

Force Field X: A Computational Microscope to Study Genetic Variation and Organic Crystals Using Theory and Experiment, R. A. Gogal, A. J. Nessler, A. C. Thiel, H. V. Bernabe, R. A. Corrigan Grove, L. M. Gousineau, J. M. Litman, J. M. Miller, G. Qi, M. J. Speranza, M. R. Tollefson, T. D. Fenn, J. J. Michaelson, O. Okada, J.-P. Piquemal, J. W. Ponder, J. Shen, R. J. H. Smith, W. Yang, P. Ren and M. J. Schnieders, J. Chem. Phys., 161, 012501 (2024) [PMCID:PMC11223778] [PDF]

Beyond Isotropic Repulsion: Classical Anisotropic Repulsion by Inclusion of p Orbitals, M. K. J. Chung and J. W. Ponder, J. Chem. Phys., 160, 174118 (2024) [PMCID:PMC11078554] [PDF]

Constant-pH Simulations with the Polarizable Atomic Multipole AMOEBA Force Field, A. C. Thiel, M. J. Speranza, S. Jadhav, L. L. Stevens, D. K. Unruh, P. Ren, J. W. Ponder, J. Shen and M. J. Schnieders, J. Chem. Theory Comput., 20, 2921-2933 (2024) [PMCID:PMC11008096] [PDF]

A Generalized Kirkwood Implicit Solvent for the Polarizable AMOEBA Protein Model, R. A. Corrigan, A. C. Thiel, J. R. Lynn, T. L. Casavant, P. Ren, J. W. Ponder and M. J. Schnieders, J. Chem. Phys., 159, 054102 (2023) [PMCID:PMC10396400] [PDF]

Accurate Host-Guest Binding Free Energies Using the AMOEBA Polarizable Force Field, M. K. J. Chung, R. J. Miller, B. Novak, Z. Wang and J. W. Ponder, J. Chem. Inf. Model., 63, 2769-2782 (2023) [PMCID:PMC10878370] [PDF]

Classical Exchange Polarization: An Anisotropic Variable Polarizability Model, M. K. J. Chung, Z. Wang, J. A. Rackers and J. W. Ponder, J. Phys. Chem. B., 126, 7579-7594 (2022) [PMCID:PMC10868659] [PDF]

Computationally Driven Discovery of SARS-CoV-2 Mpro Inhibitors: From Design to Experimental Validation, L. El Khoury, Z. Jing, A. Cuzzolin, A. Deplano, D. Loco, B. Sattarov, F. Hedin, S. Wendeborn, C. Ho, D. El Ahdab, T. Jaffrelot Inizan, M. Sturlese, A. Sosic, M. Volpiana, A. Lugato, M. Barone, B. Gatto, M. Ludovica Macchia, M. Bellanda, R. Battistutta, C. Salata, I. Kondratov, R. Iminov, A. Khairulin, Y. Mykhalonok, A. Pochepko, V. Chashka-Ratushnyi, I. Kos, S. Moro, M. Montes, P. Ren, J. W. Ponder, L. Lagardere, J.-P. Piquemal and D. Sabbadin, Chem. Sci., 13, 3674-3687 (2022) [PMCID:PMC8966641] [PDF]

Polarizable Water Potential Derived from a Model Electron Density, J. A. Rackers, R. R. Silva, Z. Wang and J. W. Ponder, J. Chem. Theory Comput., 17, 7056-7084 (2021) [PMCID:PMC8923810] [PDF]

Implicit Solvents for the Polarizable Atomic Multipole AMOEBA Force Field, R. A. Corrigan, G. Qi, A. C. Thiel, J. R. Lynn, B. D. Walker, T. L. Casavant, L. Lagardere, J.-P. Piquemal, J. W. Ponder, P. Ren and M. J. Schnieders, J. Chem. Theory Comput., 17, 2323-2341 (2021) [PMCID:PMC8126468] [PDF]

Tinker-HP: Accelerating Molecular Dynamics Simulations of Large Complex Systems with Advanced Point Dipole Polarizable Force Field Using GPUs and Multi-GPU Systems, O. Adjoua, L. Lagardere, L.-H. Jolly, A. Durocher, T. Very, I. Dupays, Z. Wang, T. J. Inizan, F. Celerse, P. Ren, J. W. Ponder and J.-P. Piquemal, J. Chem. Theory Comput., 17, 2034-2053 (2021) [PMCID:PMC8047816] [PDF]

AMOEBA Binding Free Energies for the SAMPL7 TrimerTrip Host-Guest Challenge, Y. Shi, M. L. Laury, Z. Wang and J. W. Ponder, J. Comput. Aid. Mol. Des., 35, 79-93 (2021) [PMCID:PMC7867568] [PDF]

A Structural Basis for Lithium and Substrate Binding of an Inositide Phosphatase, D. E. Dollins, J.-P. Xiong, S. Endo-Streeter, D. E. Anderson, V. S. Bansal, J. W. Ponder, Y. Ren and J. D. York, J. Biol. Chem., 296, 100059 (2021) [PMCID:PMC7948987] [PDF]

Raising the Performance of the Tinker-HP Molecular Modeling Package, L.-H. Jolly, A. Duran, L. Lagardere, J. W. Ponder, P. Ren and J.-P. Piquemal, LiveCoMS, 1, 2.10409 (2019) [PDF]

Classical Pauli Repulsion: An Anisotropic, Atomic Multipole Model, J. A. Rackers and J. W. Ponder, J. Chem. Phys., 150, 084104 (2019) [PMCID:PMC6386640] [PDF]

Absolute Binding Free Energies for the SAMPL6 Cucurbit[8]ruil Host-Guest Challenge via the AMOEBA Polarizable Force Field, M. L. Laury, Z. Wang, A. S. Gordon and J. W. Ponder, J. Comput. Aid. Mol. Des., 32, 1087-1095 (2018) [PMCID:PMC6240481] [PDF]

Tinker 8: Software Tools for Molecular Design, J. A. Rackers, Z. Wang, C. Lu, M. L. Laury, L. Lagardere, M. J. Schnieders, J.-P. Piquemal, P. Ren and J. W. Ponder, J. Chem. Theory Comput., 14, 5273-5289 (2018) [PMCID:PMC6335969] [PDF]

A Physically Grounded Damped Dispersion Model with Particle Mesh Ewald Summation, J. A. Rackers, C. Liu, P. Ren and J. W. Ponder, J. Chem. Phys., 149, 084115 (2018) [PMCID:PMC6118897] [PDF]

AMOEBA Polarizable Atomic Multipole Force Field for Nucleic Acids, C. Zhang, C. Lu, Z. Jing, C. Wu, J.-P. Piquemal, J. W. Ponder and P. Ren, J. Chem. Theory. Comput., 14, 2084-2108 (2018) [PMCID:PMC5893433] [PDF]

Tinker-HP: A Massively Parallel Molecular Dynamics Package for Multiscale Simulations of Large Complex Systems with Advanced Point Dipole Polarizable Force Fields, L. Lagardere, L.-H. Jolly, F. Lipparini, F. Aviat, B. Stamm, Z. F. Jing, M. Harger, H. Torabifard, G. A. Cisneros, M. J. Schnieders, N. Gresh, Y. Maday, P. Y. Ren, J. W. Ponder and J.-P. Piquemal, Chem. Sci., 9, 956-972 (2018) [PMCID:PMC5909332] [PDF]

Tinker-OpenMM: Absolute and Relative Alchemical Free Energies Using AMOEBA on GPUs, M. Harger, D. Li, Z. Wang, K. Dalby, L. Lagardere, J.-P. Piquemal, J. Ponder and P. Ren, J. Comput. Chem., 38, 2047-2055 (2017) [PMCID:PMC5539969] [PDF]

An Optimized Charge Penetration Model for Use with the AMOEBA Force Field, J. A. Rackers, Q. Wang, C. Liu, J.-P. Piquemal, P. Ren and J. W. Ponder, Phys. Chem. Chem. Phys., 19, 276-291 (2017) [PMCID:PMC5177509] [PDF]

Truncated Conjugated Gradient (TCG): An Optimal Strategy for the Analytical Evaluation of the Many-Body Polarization Energy and Forces in Molecular Simulations, F. Aviat, A. Levitt, B. Stamm, Y. Maday, P. Ren, J. W. Ponder, L. Lagardere and J.-P. Piquemal, J. Chem. Theory Comput., 13, 180-190 (2017) [PMCID:PMC5228058] [PDF]

Blind Prediction of Distribution in the SAMPL5 Challenge with QM based Protomer and pKa Corrections, F. C. Pickard IV, G. Konig, F. Tofoleanu, J. Lee, A. C. Simmonett, Y. Shao, J. W. Ponder and B. R. Brooks, J. Comput. Aid. Mol. Des., 30, 1087-1100 (2016) [PMID:PMC27646286] [PDF]

Calculating Binding Free Energies of Host-Guest Systems Using the AMOEBA Polarizable Force Field, D. R. Bell, R. Qi, Z. Jing, J. Y. Xiang, C. Meijas, M. J. Schnieders, J. W. Ponder and P. Ren, Phys. Chem. Chem. Phys., 18, 30261-30269 (2016) [PMCID:PMC5102783] [PDF]

An Empirical Extrapolation Scheme for Efficient Treatment of Induced Dipoles, A. C. Simmonett, F. C. Pickard IV, J. W. Ponder and B. R. Brooks, J. Chem. Phys., 145, 164101 (2016) [PMCID:PMC5085973] [PDF]

Advanced Potential Energy Surfaces for Molecular Simulation, A. Albaugh, H. A. Boateng, R. T. Bradshaw, O. N. Demerdash, J. Dziedzic, Y. Mao, D. T. Margul, J. Swails, Q. Zeng, D. A. Case, P. Eastman, L.-P. Wang, J. W. Essex, M. Head-Gordon, V. S. Pande, J. W. Ponder, Y. Shao, C.-K. Skylaris, I. T. Todorov, M. E. Tuckerman and T. Head-Gordon, J. Phys. Chem. B, 120, 9811-9832 (2016) [PMCID:PMC9113031] [PDF]

TINKTEP: A Fully Self-Consistent, Mutually Polarizable QM/MM Approach based on the AMOEBA Force Field, J. Dziedzic, Y. Mao, Y. Shao, J. Ponder, T. Head-Gordon, M. Head-Gordon and C.-K. Skylaris, J. Chem. Phys., 145, 124106 (2016) [PMID:27782640] [PDF]

Scalable Improvement of SPME Multipolar Electrostatics in Anisotropic Polarizable Molecular Mechanics Using a General Short-Range Penetration Correction up to Quadrupoles, C. Narth, L. Lagardere, E. Polack, N. Gresh, Q. Wang, D. R. Bell, J. A. Rackers, J. W. Ponder, P. Y. Ren and J.-P. Piquemal, J. Comput. Chem., 37, 494-506 (2016) [PMCID:PMC4730919] [PDF]

Polarizable Multipole-Based Force Field for Dimethyl and Trimethyl Phosphate, C. Zhang, C. Lu, Q. Wang, J. W. Ponder and P. Ren, J. Chem. Theory Comput., 11, 5326-5339 (2015) [PMCID:PMC4768686] [PDF]

General Model for Treating Short-Range Electrostatic Penetration in a Molecular Mechanics Force Field, Q. Wang, J. A. Rackers, C. He, R. Qi, C. Narth, L. Lagardere, N. Gresh, J. W. Ponder, J.-P. Piquemal and P. Ren, J. Chem. Theory Comput., 11, 2609-2618 (2015) [PMCID:PMC4570253] [PDF]

High-Resolution Crystal Structures of Protein Helices Reconciled with Three-Centered Hydrogen Bonds and Multipole Electrostatics, D. J. Kuster, C. Liu, Z. Feng, J. W. Ponder and G. R. Marshall, PLoS ONE, 10, 0123146 (2015) [PMCID:PMC4403875] [PDF]

Revised Parameters for the AMOEBA Polarizable Atomic Multipole Water Model, M. L. Laury, L.-P. Wang, V. S. Pande, T. Head-Gordon and J. W. Ponder, J. Phys. Chem. B., 119, 9423-9437 (2015) [PMCID:PMC4772747] [PDF]

Helix Stability of Oligoglycine, Oligoalanine, and Oligo-beta-Alanine Dodecamers Reflected by Hydrogen-Bond Persistence, C. Liu, J. W. Ponder and G. R. Marshall, Proteins, 82, 3043-3061 (2014) [PMCID:PMC4206583] [PDF]

An Angular Overlap Model for Cu(II) Ion in the AMOEBA Polarizable Force Field, J. Y. Xiang and J. W. Ponder, J. Chem. Theory Comput., 10, 298-311 (2014) [PMCID:PMC4102146] [PDF]

Systematic Improvement on the Classical Molecular Model of Water, L.-P. Wang, T. Head-Gordon, J. Ponder, P. Ren, J. Chodera, P. Eastman, T. J. Martinez and V. S. Pande, Biophys. J., 106, A403 (2014) [Abstract]

Polarizable Atomic Multipole-Based AMOEBA Force Field for Proteins, Y. Shi, Z. Xia, J. Zhang, R. Best, C. Wu, J. W. Ponder and P. Ren, J. Chem. Theory Comput., 9, 4046-4063 (2013) [PMCID:PMC3806652] [PDF]

Systematic Improvement of a Classical Molecular Model of Water, L.-P. Wang, T. L. Head-Gordon, J. W. Ponder, P. Ren, J. D. Chodera, P. K. Eastman, T. J. Martinez, and V. S. Pande, J. Phys. Chem. B, 117, 9956-9972 (2013) [PCMID:PMC3770532] [PDF]

A Valence Bond Model for Aqueous Cu(II) and Zn(II) Ions in the AMOEBA Polarizable Force Field, J. Y. Xiang and J. W. Ponder, J. Comput. Chem., 34, 739-749 (2013) [PMCID:PMC3584243] [PDF]

Molecular Dynamics of beta-Hairpin Models of Epigenetic Recognition Motifs, X. Zheng, C. Wu, J. W. Ponder and G. R. Marshall, J. Am. Chem. Soc., 134, 15970-15978 (2012) [PMCID:PMC3482467] [PDF]

Polarizable Atomic Multipole-based Molecular Mechanics for Organic Molecules, P. Ren, C. Wu and J. W. Ponder, J. Chem. Theory Comput., 7, 3143-3161 (2011) [PMCID:PMC3196664] [PDF]

MSCALE: A General Utility for Multiscale Modeling, H. L. Woodcock, B. T. Miller, M. Hodoscek, A. Okur, J. D. Larkin, J. W. Ponder and B. R. Brooks, J. Chem. Theory Comput., 7, 1208-1219 (2011) [PMCID:PMC3117588] [PDF]

Multipole Electrostatics in Hydration Free Energy Calculations, Y. Shi, C. Wu, J. W. Ponder and P. Ren, J. Comput. Chem., 32, 967-977 (2011) [PMCID:PMC3073856] [PDF]

Current Status of the AMOEBA Polarizable Force Field, J. W. Ponder, C. Wu, P. Ren, V. S. Pande, J. D. Chodera, D. L. Mobley, M. J. Schnieders, I. Haque, D. S. Lambrecht, R. A. DiStasio, Jr., M. Head-Gordon, G. N. I. Clark, M. E. Johnson and T. Head-Gordon, J. Phys. Chem. B, 114, 2549-2564 (2010) [PMCID:PMC2918242] [PDF]

Approaching ab Initio Complete Basis Set Limit and Experimental Accuracy for Ions in the AMOEBA Polarizable Force Field, C. Wu, P. Ren and J. W. Ponder, CCB Report 2010-01, Washington University School of Medicine (2010) [PDF]

From Data or Dogma? The Myth of the Ideal Helix, D. J. Kuster, S. Urahata, J. W. Ponder and G. R. Marshall, Biophys. J., 96, A5 (2009) [Abstract]

Polarizable Atomic Multipole Solutes in a Generalized Kirkwood Continuum, M. J. Schnieders and J. W. Ponder, J. Chem. Theory Comput., 3, 2083-2097 (2007) [PMCID:PMC4767294] [PDF]

Polarizable Atomic Multipole Solutes in a Poisson-Boltzmann Continuum, M. J. Schnieders, N. A. Baker, P. Ren and J. W. Ponder, J. Chem. Phys., 126, 124114 (2007) [PMCID:PMC2430168] [PDF]

Force Field Modeling of Conformational Energies: Importance of Multipole Moments and Intramolecular Polarization, T. D. Rasmussen, P. Ren, J. W. Ponder and F. Jensen, Int. J. Quantum Chem., 107, 1390-1395 (2007) [PDF]

Temperature and Pressure Dependence of the AMOEBA Water Model, P. Ren and J. W. Ponder, J. Phys. Chem. B, 108, 13427-13437 (2004) [PMCID:PMC2855697] [PDF]

Ion Solvation Thermodynamics from Simulation with a Polarizable Force Field, A. Grossfield, P. Ren and J. W. Ponder, J. Am. Chem. Soc., 125, 15671-15682 (2003) [PMID:14664617] [PDF]

Force Fields for Protein Simulation, J. W. Ponder and D. A. Case, Adv. Prot. Chem., 66, 27-85 (2003) [PMID:14631816] [PDF]

Polarizable Atomic Multipole Water Model for Molecular Mechanics Simulation, P. Ren and J. W. Ponder, J. Phys. Chem. B, 107, 5933-5947 (2003) [PDF]

Consistent Treatment of Inter- and Intramolecular Polarization in Molecular Mechanics Calculations, P. Ren and J. W. Ponder, J. Comput. Chem., 23, 1497-1506 (2002) [PMID:12395419] [PDF]

Global Optimization via a Modified Potential Smoothing Kernel, A. Grossfield and J. W. Ponder, CCB Report 2002-01, Washington University School of Medicine (2002) [PDF]

Turn Scanning: Experimental and Theoretical Approaches to the Role of Turns, C. Frieden, E. S. Huang and J. W. Ponder, in Protein Folding and Stability, K. Murphy, Ed., Humana Press Inc., Totowa, New Jersey, April 2001, Chapter 7, pages 133-158 [PMID:11357623] [PDF]

Exploring the Similarities between Potential Smoothing and Simulated Annealing, R. K. Hart, R. V. Pappu and J. W. Ponder, J. Comput. Chem., 21, 531-552 (2000) [PDF]

Binding of Retinol Induces Changes in Rat Cellular Retinol-binding Protein II Conformation and Backbone Dynamics, J. Lu, C.-L. Lin, C. Tang, J. W. Ponder, J. L. F. Kao, D. P. Cistola and E. Li, J. Mol. Biol., 300, 619-632 (2000) [PMID:10884357] [PDF]

CASP3 ab Initio Protein Structure Prediction Results Using a Simple Distance Geometry-Based Method, E. S. Huang, R. Samudrala and J. W. Ponder, CCB Report 1999-01, Washington University School of Medicine (1999) [PDF]

Ab initio Fold Prediction of Small Helical Proteins Using Distance Geometry and Knowledge-Based Scoring Functions, E. S. Huang, R. Samudrala and J. W. Ponder, J. Mol. Biol., 290, 267-281 (1999) [PMID:10388572] [PDF]

A Potential Smoothing Algorithm Accurately Predicts Transmembrane Helix Packing, R. V. Pappu, G. R. Marshall and J. W. Ponder, Nature Struct. Biol., 6, 50-55 (1999) [PMID:9886292] [PDF]

The Structure and Dynamics of Rat Apo-Cellular Retinol-Binding Protein II in Solution: Comparison with the X-ray Structure, J. Lu, C.-L. Lin, C. Tang, J. W. Ponder, J. Kao, D. P. Cistola and E. Li, J. Mol. Biol., 286, 1179-1195 (1999) [PMID:10047490] [PDF]

Analysis and Application of Potential Energy Smoothing for Global Optimization, R. V. Pappu, R. K. Hart and J. W. Ponder, J. Phys. Chem. B, 102, 9725-9742 (1998) [PDF]

Hierarchical Conformational Scanning Using Potential Smoothing. Application to Cycloheptadecane, R. V. Pappu, R. K. Hart and J. W. Ponder, CCB Report 1998-01, Washington University School of Medicine (1998) [PDF]

Distance Geometry Generates Native-like Folds for Small Helical Proteins using Consensus Distances of Predicted Protein Structures, E. S. Huang, R. Samudrala and J. W. Ponder, Prot. Sci., 7, 1998-2003 (1998) [PMID:9761481] [PDF]

Generalized Potential Function Smoothing Algorithms for Conformational Energy Optimization, R. K. Hart, R. V. Pappu and J. W. Ponder, Biophys. J., 74, A176 (1998) [Abstract]

Accuracy of Side-Chain Prediction upon Near-Native Protein Backbones Generated by ab Initio Folding Methods, E. S. Huang, P. Koehl, M. Levitt, R. V. Pappu and J. W. Ponder, Proteins, 33, 204-217 (1998) [PMID:9779788] [PDF]

Light-Activated Rhodopsin Induces Structural Binding Motif in G-Protein alpha Subunit, O. Kisselev, J. Kao, J. W. Ponder, Y. C. Fann, N. Gautam and G. R. Marshall, Proc. Nat. Acad. Sci. USA, 95, 4270-4275 (1998) [PMCID:22478] [PDF]

Protein Structure Prediction Using a Combination of Sequence Homology and Global Energy Minimization II. Energy Functions, M. J. Dudek, K. Ramnarayan and J. W. Ponder, J. Comput. Chem., 19, 548-573 (1998) [PDF]

Type 2M von Willebrand Disease: F606I and I662F Mutations in the Glycoprotein Ib Binding Domain Selectively Impair Ristocetin- but not Botrocetin-mediated Binding of von Willebrand Factor to Platelets, C. A Hillery, D. J. Mancuso, J. E. Sadler, J. W. Ponder, M. L. Jozwiak, P. A. Christopherson, J. C. Gill, J. P. Scott and R. R. Montgomery, Blood, 91, 1572-1581 (1998) [PMID:9473222] [PDF]

Calculation of the Reaction Field due to Off-Center Point Multipoles, Y. Kong and J. W. Ponder, J. Chem. Phys., 107, 481-492 (1997) [PDF]

The NMR Solution Structure of Intestinal Fatty Acid-binding Protein Complexed with Palmitate: Application of a Novel Distance Geometry Algorithm, M. E. Hodsdon, J. W. Ponder and D. P. Cistola, J. Mol. Biol., 264, 585-602 (1996) [PMID:8969307] [PDF]

Accurate Modeling of the Intramolecular Electrostatic Energy of Proteins, M. J. Dudek and J. W. Ponder, J. Comput. Chem., 16, 791-816 (1995) [PDF]

Definition of a Metal-Dependent/Li+-Inhibited Phosphomonoesterase Protein Family based upon a Conserved Three-dimensional Core Structure, J. D. York, J. W. Ponder and P. W. Majerus, Proc. Nat. Acad. Sci. USA, 92, 5149-5153 (1995) [PMID:7761465] [PDF]

Crystal Structure of Inositol Polyphosphate 1-Phosphatase at 2.3 Å Resolution, J. D. York, Z.-W. Chen, J. W. Ponder, F. S. Matthews and P. W. Majerus, Biochemistry, 33, 13164-13171 (1994) [PMID:7947723] [PDF]

Crystallization and Initial X-ray Crystallographic Characterization of Recombinant Bovine Inositol Polyphosphate 1-Phosphatase Produced in Spodoptera frugiperda Cells, J. D. York, Z. W. Chen, J. W. Ponder, A. K. Chauhan, F. S. Matthews and P. W. Majerus, J. Mol. Biol., 236, 584-589 (1994) [PMID:8107142] [PDF]

Differential Binding of Retinol Analogs to Two Homologous Cellular Retinol-Binding Proteins, D. Rong, A. J. Lovey, M. Rosenberger, A. d'Avignon, J. Ponder and E. Li, J. Biol. Chem., 268, 7929-7934 (1993) [PMID:8463314] [PDF]

Algorithms for Calculating Excluded Volume and its Derivatives as a Function of Molecular Conformation and Their Use in Energy Minimization, C. E. Kundrot, J. W. Ponder and F. M. Richards, J. Comput. Chem., 12, 402-409 (1991) [PDF]

The Use of Tertiary Templates in the Analysis of Favorable Helix-Helix Packing Sites, J. W. Ponder and F. M. Richards, J. Cellular Biochem., 13A, 59 (1989) [Abstract]

Internal Packing and Protein Structural Classes, J. W. Ponder and F. M. Richards, Cold Spring Harbor Symposia on Quantitative Biology, 52, 421-428 (1987) [PMID:2841069] [PDF]

An Efficient Newton-Like Method for Molecular Mechanics Energy Minimization of Large Molecules, J. W. Ponder and F. M. Richards, J. Comput. Chem., 8, 1016-1026 (1987) [PDF]

Tertiary Templates for Proteins: Use of Packing Criteria in the Enumeration of Allowed Sequences for Different Structural Classes, J. W. Ponder and F. M. Richards, J. Mol. Biol., 193, 775-791 (1987) [PMID:2441069] [PDF]

Stereochemistry of the Hygrolidins, E. J. Corey and J. W. Ponder, Tetrahedron Letters, 25, 4325-4328 (1984) [PDF]

The Stereochemistry and Biosynthesis of Hybridalactone, an Eicosanoid from Laurencia hybrida, E. J. Corey, B. De, J. W. Ponder and J. M. Berg, Tetrahedron Letters, 25, 1015-1018 (1984) [PDF]

Synthesis of a Stable Analog of Thromboxane A2 with Methylene Replacing the 9,11-Bridging Oxygen, E. J. Corey, J. W. Ponder and P. Ulrich, Tetrahedron Letters, 21, 137-140 (1980) [PDF]

Metal-Ammonia Reduction of Triptycene and Related Benzobarrelene Derivatives, P. W. Rabideau, D. W. Jessup, J. W. Ponder and G. F. Beekman, J. Org. Chem., 44, 4594-4597 (1979) [PDF]

The Synthesis of 4-Methyl-3-heptanol and 4-Methyl-3-heptanone: Two Easily Synthesized Insect Pheremones, R. M. Einterz, J. W. Ponder and R. S. Lenox, J. Chem. Educ., 54, 382-383 (1977) [PDF]

Moses Kwang Jin Chung, Development and Applications of a Physics-Based Force Field, Department of Physics, Washington University, Saint Louis, MO, April 2024 [PDF]

Roseane dos Reis Silva, A Quantum Physics-Based Force Field for Biomolecular Simulation, Computational & Molecular Biophysics Program, Washington University, Saint Louis, MO December 2023 [PDF]

Joshua A. Rackers, A Physics-Based Intermolecular Potential for Biomolecular Simulation, Computational & Molecular Biophysics Program, Washington University, Saint Louis, MO April 2019 [PDF]

Zhi Wang, Polarizable Force Field Development, and Applications to Conformational Sampling and Free Energy Calculations, Department of Chemistry, Washington University, Saint Louis, MO, August 2018 [PDF]

Jin Yu (Justin) Xiang, Development of Polarizable Force Field Models for Transition Metal Ions, Computational & Molecular Biophysics Program, Washington University, Saint Louis, MO, May 2013 [PDF]

Michael J. Schnieders, The Theory and Effect of Solvent Environment on Biomolecules, Department of Biomedical Engineering, Washington University, Saint Louis, MO, December 2007 [PDF]

Reece K. Hart, Potential Function Smoothing with Application to Molecular Docking, Molecular Biophysics Program, Washington University, Saint Louis, MO, December 1998 [PDF]

Yong Kong, Multipole Electrostatic Methods for Protein Modeling with Reaction Field Treatment, Molecular Biophysics Program, Washington University, Saint Louis, MO, August 1997 [PDF]

Jay W. Ponder, I. Synthesis of a Thromboxane A2 Analog, II. Conformational Analysis of Arachadonic Acid, III. Conformational Analysis of Medium-Ring Natural Products, Department of Chemistry, Harvard University, Cambridge, MA, August 1984 [PDF]