Research Goals

    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, organic chemistry and materials science. We have written suites of computer programs ranging from macromolecular mechanics and dynamics simulation (TINKER) to empirical packing analysis of protein structure (PROPAK) to sequence level analysis (SLEUTH) and ab initio protein structure prediction (using DISTGEOM). Recently our work has centered on the parameterization and validation of the AMOEBA polarizable atomic multipole force field, and on efficient conformational search algorithms for simplified potential energy surfaces.


Publication List

    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) [PDF]

    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:PCM3770532] [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]

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

    A 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. Samdrula 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:PMC22478] [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 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]


Doctoral Dissertations

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

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

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

    Yong Kong, Multipole Electrostatic Methods for Protein Modeling with Reaction Field Treatment, Molecular Biophysics Program, Washington University, St. 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, Chemistry Department, Harvard University, Cambridge, MA, August 1984 [PDF]



Last Update: February 16, 2014
Maintainer: webmaster@dasher.wustl.edu (sendmail)