Jay Ponder Lab

Force Field Explorer

    Our group is primarily interested in computational chemistry, especially the development of new algorithms and their application to problems in structural biology and organic chemistry. We develop, maintain and distribute several software packages which are described below. Publications and doctoral dissertations from the lab are available from Jay Ponder's Home Page.

Software Distributed by the Lab

  • TINKER: A complete package for molecular mechanics, dynamics and modeling of molecules, especially biomacromolecules. Tinker has the ability to use any of several common parameter sets, such as Amber (ff94, ff96, ff98, ff99), CHARMM (19, 22 and 22-CMAP), Allinger MM (MM2-1991 and MM3-2000), OPLS (OPLS-UA, OPLS-AA and OPLS-AA/L), as well as our AMOEBA polarizable atomic multipole force field. Tinker implements a variety of novel algorithms including distance geometry with fast metrization and Gaussian trial distances, Elber's reaction path method, global optimization via our Potential Smoothing and Search algorithms, molecular dynamics with simulated annealing and stochastic dynamics options, particle mesh Ewald summation, Monte Carlo minimization, atomic multipole treatment of electrostatics with explicit dipole polarizability, Eisenberg-McLachlan ASP and GB/SA continuum solvation models, and truncated Newton TNCG local energy minimization.

  • FORCE FIELD EXPLORER: A Java-based GUI for Tinker, which includes molecular visualization as well as the ability to launch Tinker calculations from a graphical interface. FFE uses a socket mechanism for communication between the GUI and Tinker programs, allowing local monitoring of jobs running on remote machines. The program can also download organics and drugs from PubChem and the NCI, and biopolymer structures from the PDB.

  • SLEUTH: A small set of programs that allow creation of PDB file summaries and searching of a dataset extracted from the PDB for structural motifs. For example, SLEUTH can find all examples of type I turns that match some generalized sequence pattern. An additional program implements the Eisenberg 3D profile algorithm. The /data subdirectory contains a set of summary files with dihedral angle values, secondary structure and solvent exposure data by residue for many of the current PDB structures.

  • PROPAK: A program to attack the "inverse" protein folding problem via modeling of the side chain packing in proteins. Allows the user to redesign a portion of a known structure using a library of side chain rotamers. Provides a list of the amino acid sequences that are predicted be compatable with an input tertiary fold. The PROPAK algorithm was one of the first attempts to attack this general protein design problem. The original program, although still useful, has not been under active development for some time and is largely superceded by methods from the labs of Steve Mayo, David Baker, and many others.

  • QSAR: A program to derive QSAR models via regression analysis. The analysis can be performed by ordinary least squares (OLS), principal components (PCR) or partial least squares (PLS). "Leave-1-out" cross-validation is performed for all three types of analysis. For OLS and PCR, variable selection can be performed via simulated annealing on predictive power. In all cases, the final QSAR model can be used to make predictions for a test set distinct from the training set. Several training set data tables, including Garland Marshall's VALIDATE set for prediction of binding in macromolecular complexes, are provided as examples.

Teaching & Course Information

Group Meeting Presentations

  • Host-Guest Ligand Binding Systems (Jay Ponder, December 03) [PDF]

  • Water Diffusion in NaCl/CsI Solutions (Zhi Wang, June 11) [PDF]

  • Why the Sulfinyl Group is Special in DMSO (Chao Lu, June 04) [PDF]

  • Strange Case of Enthalpy-Entropy Compensation (Jay Ponder, May 28) [PDF]

  • Protein Structure from Correlated Mutations (Brooke Husic, May 16) [PDF]

Principal Investigator

  • Jay Ponder
    Professor, Chemistry, Biomedical Engineering,
    and Biochemistry & Molecular Biophysics
    Washington University
  • Current Group Members

  • Zhi Wang
    Research Associate, Chemistry
    Washington University
  • Roseane Dos Reis Silva
    Graduate Student, DBBS
    Biochemistry, Biophysics & Structural Biology
    Washington University

  • Moses Chung
    MSTP Student, Physics
    Washington University School of Medicine
  • Ryan Miller
    Undergraduate, Chemistry & Computer Science
    Washington University

  • Former Group Members

  • Yuanjun "Sherlock" Shi
    Graduate Student, Chemistry
    Yale University
  • Borna Novak
    MSTP Student
    Washington University School of Medicine

  • Marie Laury
    Bioinformatics Scientist, GTAC
    Washington University School of Medicine
  • Josh Rackers
    Harry S. Truman Fellow
    Sandia National Laboratories

  • Aaron Gordon
    Software Engineer
    Boeing, Defense, Space & Security, St. Louis
  • Chao Lu
    Senior Scientist
    Schrodinger, LLC, New York, NY

  • Kailong Mao
    Associate Software Engineer
    Allscripts Healthcare Solutions, Raleigh, NC
  • Brendan McMorrow
    Science Engineer
    DeepMind Technologies Limited, London

  • Brooke Husic
    Fellow, Center for Theoretical Science
    Princeton University
  • Pooja Suresh
    Graduate Student, Biophysics
    University of California, San Francisco

  • Laura Watkins
    Graduate Student, Chemistry
    University of Chicago
  • Justin Xiang
    Chief Investment Officer
    Syno Capital, New York, NY

  • Chris Mejias
    Resident Physician
    Barnes-Jewish Hospital, Saint Louis, MO
  • Tyler Ponder
    Software Engineer, AWS S3 Storage
    Amazon Web Services, Seattle, WA

  • Jeffrey Bigg
    Software Engineer
    Propel, Inc., Brooklyn, NY
  • Victoria Wang
    Medical Student, Pritzker School of Medicine
    University of Chicago

  • Yong Huang
    ETL and Data Conversion Engineer
    Three Rivers Systems, Inc.
  • Dave Gohara
    Research Professor, Biochemistry & Molecular Biology
    Saint Louis University

  • Chuanjie Wu
    Head, Force Field Development
    Roivant Discovery, New York, NY
  • Sergio Urahata
    Institute of Physics
    University of Sao Paulo, Brazil

  • Mike Schnieders
    Associate Professor, Biomedical Engineering
    University of Iowa
  • Pengyu Ren
    Professor, Biomedical Engineering
    University of Texas, Austin

  • Alan Grossfield
    Associate Professor, Biochemistry & Biophysics
    University of Rochester Medical School
  • Peter Bagossi
    Associate Professor, Biochemistry & Molecular Biology
    University of Debrecen, Hungary

  • Enoch Huang
    Vice President, Machine Learning & Computational Sciences
    Pfizer R&D, Cambridge, MA
  • Reece Hart
    Chief Scientist, Genome Commons
    University of California, Berkeley

  • Rohit Pappu
    Professor, Biomedical Engineering
    Washington University, St. Louis
  • Yong Kong
    Associate Director, Bioinformatics
    W. M. Keck Foundation Laboratory, Yale University

  • Megan Fedders
    Director, Analytics & Informatics
    Cigna Onsite Health
  • Mike Dudek
    Founder & Chief Scientist
    Hexadecapole, San Diego, CA

  • Margaret Goodman
    Professor, Biology
    Wittenberg University
  • Uma Kuchibhotla
    Chief Scientific Officer, Biotechnology
    Eli Lilly and Company

  • Last Update: March 30, 2022
    Maintainer: ponder@dasher.wustl.edu (send mail)