Jay Ponder
Professor, Chemistry, Biochemistry & Molecular Biophysics, And Biomedical Engineering at Washington University in St. Louis
Missouri, United States
Summary
👤
Senior🎓
Top SchoolJay Ponder is a professor and computational chemist with over three decades of experience developing molecular simulation methods and advanced force fields, and he currently holds appointments in Chemistry, Biochemistry & Molecular Biophysics, and Biomedical Engineering at Washington University in St. Louis. He is the original developer of the Tinker molecular modeling package and leads research in physics-based drug design, binding free energy calculations, and polarizable multipole potentials. As founder and consultant of Qubit Pharmaceuticals, he bridges academic method development with industrial lead optimization and is exploring the transition from classical modeling toward quantum computing approaches. His background spans rigorous theoretical chemistry (Ph.D. Harvard) and hands-on software engineering, reflecting a blend of synthesis, computation, and tool-building. Known for mentoring across disciplines, he brings rare depth in both algorithmic innovation and practical application to drug discovery.
11 years of coding experience
1 year of employment as a software developer
B.A., Mathematics, and Chemistry, B.A., Mathematics, and Chemistry at Wabash CollegePh.D., Dept. of Chemistry, Natural Product Synthesis, Ph.D., Dept. of Chemistry, Natural Product Synthesis at Harvard UniversityPostdoctoral, Dept. of Molecular Biophysics & Biochemistry, Computational Biophysics, Postdoctoral, Dept. of Molecular Biophysics & Biochemistry, Computational Biophysics at Yale
Github Skills (20)
simulation10
dft10
molecular-simulation10
gpu10
tinker10
cuda10
high-performance10
java9
evolution9
sbml9
parallel7
python7
prediction7
opencl7
parameterization6
Programming languages (4)
Github contributions (5)
TinkerTools/tinker-openmm
Nov 2020 - Mar 2021
Tinker-OpenMM: An OpenMM Version Enabling Tinker on GPUs
Contributions:36 commits, 18 pushes, 1 issue in 3 months
cudatinkeropenmmgpugpus
TinkerTools/tinker
Mar 2016 - Jan 2023
Tinker: Software Tools for Molecular Design
Contributions:1 release, 5 reviews, 828 commits in 6 years 11 months
tinkermolecular-dynamicssoftware-toolsmolecularmolecular-mechanics
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