TINKER

Jay Ponder Lab

Force Field Explorer

    Our group is primarily interested in computational chemistry, especially the development of new models and 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 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, St. Louis, MO
    ponder@dasher.wustl.edu
  • Current Group Members

  • Moses Chung
    Medical Scientist Training Program, and Physics
    Washington University School of Medicine, St. Louis, MO
    kchung25@wustl.edu
  • Zhecheng He
    Postdoctoral Associate, Chemistry
    Washington University, St. Louis, MO
    hzhecheng@gmail.com


  • Former Group Members

  • Nick Hatzis-Schoch
    Graduate Student, Chemistry
    Yale University, New Haven, CT
    h.nicholas@wustl.edu

  • Zhi Wang
    Research Scientist
    ByteDance, Bellevue, WA
    wangzhi@wustl.edu
  • Roseane Dos Reis Silva
    Research Scientist, Computational Chemistry
    Qubit Pharmaceuticals, Boston, MA
    roseane@wustl.edu

  • Ryan Miller
    Graduate Student, Computer Science
    University of California, Irvine, CA
    ryan.miller@wustl.edu
  • Chris Ho
    Senior Research Scientist
    Qubit Pharmaceuticals, Boston, MA
    cho@newdrugdesign.com

  • Yuanjun "Sherlock" Shi
    Graduate Student, Chemistry
    Yale University, New Haven, CT
    yuanjun@wustl.edu
  • Borna Novak
    Medical Scientist Training Program
    Washington University School of Medicine, St. Louis, MO
    bnovak@wustl.edu

  • Marie Laury
    Bioinformatics Scientist, GTAC
    Washington University School of Medicine, St. Louis, MO
    majkutml@gmail.com
  • Josh Rackers
    Machine Learning Scientist
    Prescient Design, New York, NY
    joshrackers@gmail.com

  • Aaron Gordon
    Software Engineer
    Boeing, Seattle, WA
    aarongordon@wustl.edu
  • Chao Lu
    Lead, Force Field Development
    ByteDance, New York, NY
    chaolupersonal@gmail.com

  • Kailong Mao
    Back-End Software Engineer
    Allscripts Healthcare Solutions, Raleigh, NC
    kailong.mao@gmail.com
  • Brendan McMorrow
    Staff Software Engineer
    DeepMind Technologies Limited, London, England
    mcmobc2@gmail.com

  • Brooke Husic
    Sigler Scholar, Center for Physics of Biological Function
    Princeton University, Princeton, NJ
    brookehusic@gmail.com
  • Pooja Suresh
    Biophysicist & Data Scientist
    CytoTronics, Inc., Boston, MA
    pooja.suresh@ucsf.edu

  • Laura Watkins
    Data Scientist, Kemper
    Chicago, IL
    lcwatkins21@gmail.com
  • Justin Xiang
    Chief Investment Officer
    Syno Capital, New York, NY
    justin.xiang@synocapital.com

  • Chris Mejias
    Fellow, Abdominal Radiology
    University of Washington, Seattle, WA
    mejiasc@wusm.wustl.edu
  • Tyler Ponder
    Software Engineer, AWS Cloud Security
    Amazon Web Services, New York, NY
    tponder11@gmail.com

  • Jeffrey Bigg
    Lead Cyber Engineer
    MITRE Corporation, Bedford, MA
    jbigg.2012@gmail.com
  • Victoria Wang
    GYN ONC Fellow, Brigham & Women's Hospital
    Boston, MA
    victoria.wang.912@gmail.com

  • Yong Huang
    Senior Manager, Software Deveolopment
    Charter Communications, St. Louis, MO
    yhuang01@gmail.com
  • Dave Gohara
    Consultant, Biochemistry
    St. Louis University, St. Louis, MO
    dgohara@slu.edu

  • Chuanjie Wu
    Research Leader
    Schrodinger, New York, NY
    chuanjiewu@gmail.com
  • Sergio Urahata
    Institute of Physics
    University of Sao Paulo, Brazil
    surahata@gmail.com

  • Mike Schnieders
    Professor, Biomedical Engineering, and Biochemistry
    University of Iowa
    michael-schnieders@uiowa.edu
  • Pengyu Ren
    Professor, Biomedical Engineering
    University of Texas, Austin
    pren@mail.utexas.edu

  • Alan Grossfield
    Associate Professor, Biochemistry & Biophysics
    University of Rochester Medical School
    alan_grossfield@urmc.rochester.edu
  • Peter Bagossi (deceased 2011)
    Associate Professor
    Biochemistry & Molecular Biology
    University of Debrecen, Hungary

  • Enoch Huang
    Vice President, Machine Learning & Computational Sciences
    Pfizer R&D, Cambridge, MA
    enoch_huang@cambridge.pfizer.com
  • Reece Hart
    Chief Technology Officer, MyOme
    Palo Alto, California
    reecehart@gmail.com

  • Rohit Pappu
    Professor, Biomedical Engineering
    Washington University, St. Louis, MO
    pappu@wustl.edu
  • Yong Kong
    Associate Director, Bioinformatics
    W. M. Keck Foundation Laboratory, Yale University
    yong_kong@yale.edu

  • Megan Fedders
    Director, Analytics & Value Management
    Evernorth Direct Health, Hartland, WI
    meganfedders@yahoo.com
  • Mike Dudek
    Founder & Chief Scientist
    Hexadecapole, San Diego, CA
    mdudek@hexadecapole.com

  • Margaret Goodman
    Professor, Biology
    Wittenberg University, Springfield, OH
    mgoodman@wittenberg.edu
  • Uma Kuchibhotla
    Chief Scientific Officer, Biotechnology
    Eli Lilly and Company
    kuchibhotla_uma@lilly.com


  • Last Update: November 11, 2024
    Maintainer: ponder@dasher.wustl.edu (send mail)