TINKER

Jay Ponder Lab

Force Field Explorer

    Welcome to the Home Page for the Jay Ponder Lab in the Department of Chemistry at Washington University in Saint Louis, Missouri. We are located in the Louderman Chemistry building on the Danforth campus.

    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.

  • 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

  • Protein Structure from Correlated Mutations (Brooke Husic, 16 May 2014) [PDF]

  • The Strange Case of Enthalpy-Entropy Compensation (Jay Ponder, 28 May 2014) [PDF]

  • Why the Sulfinyl Group is Special in DMSO (Chao Lv, 04 June 2014) [PDF]

  • Water Diffusion in NaCl/CsI Solutions (Zhi Wang, 11 June 2014) [PDF]


Current Ponder Group Members

  • Jay Ponder
    Principal Investigator, Chemistry
    Washington University
    ponder@dasher.wustl.edu

  • Chao Lv
    Postdoctoral Fellow, Chemistry
    Washington University
    clv@dasher.wustl.edu
  • Marie Laury
    Postdoctoral Fellow, Chemistry
    Washington University
    majkutml@gmail.com

  • Brooke Husic
    Research Technician, Chemistry
    Washington University
    brookehusic@gmail.com
  • Zhi Wang
    Graduate Student, Chemistry
    Washington University
    wangzhi@wustl.edu

  • Josh Rackers
    Graduate Student, Biophysics Program
    Division of Biology & Biomedical Sciences
    Washington University
    joshrackers@gmail.com
  • Laura Watkins
    Undergraduate Summer Student, Chemistry
    Washington University
    lcwatkins21@gmail.com

  • Pooja Suresh
    Undergraduate Summer Student, Physics
    University of Rochester
    psuresh2@u.rochester.edu


  • Former Group Members (with Current Affiliation)

  • Justin Xiang
    Senior Scientist
    Schrodinger, LLC, New York, NY
    justin.xiang@gmail.com
  • Chris Mejias
    Undergraduate Student, Chemistry
    Washington University
    christophermejias@go.wustl.edu

  • Tyler Ponder
    Undergraduate Student, Chemical Engineering
    Washington University
    tponder@wustl.edu
  • Jeff Bigg
    Undergraduate Student, Computer Engineering
    University of Illinois
    jbigg.2012@gmail.com

  • Victoria Wang
    Medical Student
    Washington University School of Medicine
    v.wang@wustl.edu
  • Yong Huang
    Research Scientist, Radiation Oncology
    Washington University School of Medicine
    yhuang01@gmail.com

  • Dave Gohara
    Research Professor, Biochemistry & Molecular Biology
    Saint Louis University
    dgohara@slu.edu
  • Chuanjie Wu
    Senior Scientist
    Schrodinger, LLC, New York, NY
    chuanjie.wu@schrodinger.com

  • Sergio Urahata
    Institute of Physics
    University of Sao Paulo, Brazil
    surahata@gmail.com
  • Mike Schnieders
    Assistant Professor, Biomedical Engineering
    University of Iowa
    michael-schnieders@uiowa.edu

  • Pengyu Ren
    Associate Professor, Biomedical Engineering
    University of Texas, Austin
    pren@mail.utexas.edu
  • Alan Grossfield
    Assistant Professor, Biochemistry & Biophysics
    University of Rochester Medical School
    alan_grossfield@urmc.rochester.edu

  • Peter Bagossi
    Associate Professor, Biochemistry & Molecular Biology
    University of Debrecen, Hungary
    bagossi@med.unideb.hu
  • Enoch Huang
    Executive Director, Computational Sciences
    Pfizer Research Technology Center
    enoch_huang@cambridge.pfizer.com

  • Reece Hart
    Chief Scientist, Genome Commons
    University of California, Berkeley
    reece@harts.net
  • Rohit Pappu
    Professor, Biomedical Engineering
    Washington University, St. Louis
    pappu@wustl.edu

  • Yong Kong
    Associate Director, Bioinformatics
    W. M. Keck Foundation Laboratory, Yale University
    yong_kong@yale.edu
  • Megan Fedders
    Project Manager, Informatics
    Medical College of Wisconsin
    meganfedders@yahoo.com

  • Mike Dudek
    Software Developer
    Biomolecule Objects LLC
    mdudek@biomoleculeobjects.com
  • Margaret Goodman
    Professor, Cell & Molecular Biology
    Wittenburg University
    mgoodman@wittenberg.edu

  • Uma Kuchibhotla
    Chief Scientific Officer
    Biotherapeutics Lead Optimization
    Eli Lilly and Company



  • Last Update: 29 May 2014
    Maintainer: ponder@dasher.wustl.edu (send mail)