Jay W. Ponder, PhD

Associate Professor
Biochemistry and Molecular Biophysics
Biomedical Engineering

Biochemistry, Biophysics, and Structural Biology Program
Computational and Systems Biology Program

  • 314-935-4275

  • 314-935-4481

  • Louderman 453, Chemistry Dept., One Brookings Drive

  • ponder@wustl.edu

  • http://dasher.wustl.edu

  • molecular modeling, protein structure, computational chemistry, molecular dynamics simulation, protein engineering

  • Computational chemistry, protein engineering, theoretical protein structure and folding

Research Abstract:

My group develops and applies computational tools for problems in structural biology and in protein engineering, function and folding. The Ponder Lab produces and distributes software packages ranging from macromolecular mechanics and dynamics simulation (TINKER) to molecular visualization (Force Field Explorer) to empirical packing analysis of protein structure (PROPAK) to sequence analysis and tertiary structure prediction (SLEUTH). Our current research focuses on two main areas related to biopolymer modeling. First, we have implemented efficient methods for including multipole electrostatics and polarization in simulations as a framework for our next-generation AMOEBA force field. This new energy model enables reliable calculation of structures and has significant advantages over traditional fixed partial atomic charge models such as Amber and CHARMM. It also yields energetics for ligand docking and drug design to within "chemical accuracy"--absolute errors of 0.5 kcal/mol or less. Current AMOEBA applications include free energy calculations of binding interactions, elucidation of the role of ions in biology, and refinement of highly accurate homology models. Second, we are exploring various powerful approaches to conformational search for flexible biopolymers. One method transforms the potential energy surface for a molecule by a diffusion equation-based smoothing procedure. This "potential smoothing" paradigm is applicable to a variety of problems including transmembrane helix packing, global optimization, and energy-based clustering of conformations. Another search method is based on a novel distance geometry algorithm and heuristic rules as a basis for protein structure prediction. Statistical distance distributions and predicted secondary structure constraints generate libraries of candidate folds to be scored with an informatics-based contact function or physics-based effective mean force potential. Ultimately, our interest in conformational search lies in the "end game" of protein folding--in making a connection between atomic-level protein structures and low-resolution models available from fold recognition algorithms.

Selected Publications:

Ren P, Wu C and Ponder JW. Polarizable Atomic Multipole-based Molecular Mechanics for Organic Molecules. Journal of Chemical Theory and Computation 2011 7: 3143-3161.

Woodcock HL, Miller BT, Hodoscek M, Okur A, Larkin JD, Ponder JW and Brooks BR. MSCALE: A General Utility for Multiscale Modeling. Journal of Chemical Theory and Computation 2011 7: 1208-1219.

Shi Y, Wu C, Ponder JW and Ren P. Multipole Electrostatics in Hydration Free Energy Calculations. Journal of Computational Chemistry 2011 32: 967-977.

Ponder JW, Wu C, Ren P, Pande VS, Chodera JD, Mobley DL, Schnieders MJ, Haque I, Lambrecht DS, DiStasio Jr. RA, Head-Gordon M, Clark GNI, Johnson ME and Head-Gordon T. Current Status of the AMOEBA Polarizable Force Field. Journal of Physical Chemistry B 2010 114: 2549-2564.

Schnieders MJ and Ponder JW. Polarizable Atomic Multipole Solutes in a Generalized Kirkwood Continuum. Journal of Chemical Theory and Computation, 3:2083-2097.

Rasmussen TD, Ren P, Ponder JW and Jensen F. Force Field Modeling of Conformational Energies: Importance of Multipole Moments and Intramolecular Polarization. International Journal of Quantum Chemistry 2007 107:1390-1395.

Grossfield A, Ren P and Ponder JW. Ion Solvation Thermodynamics from Simulation with a Polarizable Force Field. Journal of the American Chemical Society 2003 125:15671-15682.

Ponder JW and Case DA. Force Fields for Protein Simulation. Advances in Protein Chemistry 2003 66: 27-85.

Last Updated: 12/30/2011 1:38:52 PM

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