World's Best Scientists 2026 revealed!

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Chemistry

D-Index
113
Citations
59800
World Ranking
691
National Ranking
283

Molecular Biology

D-Index
115
Citations
61420
World Ranking
301
National Ranking
181

Research.com Recognitions

  • 2008 - Fellow of American Physical Society (APS) Citation For farreaching contributions to the quantitative distributed simulation, analysis, and understanding of kinetics and thermodynamics of biomolecular conformations and interactions, especially in the areas of protein folding and the role of water in confined environments

Overview

Vijay S. Pande is affiliated with Stanford University in the United States and conducts research primarily in the field of Biochemistry, Genetics, and Molecular Biology. Their work spans several subfields, including Molecular Biology, Materials Chemistry, Public Health, Environmental and Occupational Health, Computational Theory and Mathematics, and Atomic and Molecular Physics and Optics.

The scientist's research focuses on a range of topics, notably Protein Structure and Dynamics, Machine Learning in Materials Science, Computational Drug Discovery Methods, Genetics, Bioinformatics, and Biomedical Research. Additional research interests include Mosquito-borne Diseases and Control, Malaria Research and Control, and HIV Research and Treatment.

Recent published papers include:

  • OpenMM 8: Molecular Dynamics Simulation with Machine Learning Potentials, 2023, The Journal of Physical Chemistry B
  • Improvement in ADMET Prediction with Multitask Deep Featurization, 2020, Journal of Medicinal Chemistry
  • Folding@home: Achievements from over 20 years of citizen science herald the exascale era, 2023, Biophysical Journal
  • OpenMM 8: Molecular Dynamics Simulation with Machine Learning Potentials, 2023, arXiv (Cornell University)
  • Computational IR Spectroscopy of Insulin Dimer Structure and Conformational Heterogeneity, 2021, The Journal of Physical Chemistry B

Frequent co-authors in their publications include:

  • Peter Eastman
  • Raimondas Galvelis
  • Raúl P. Peláez
  • Charlles R. A. Abreu
  • Stephen E. Farr

Publications by this researcher commonly appear in venues such as:

  • The Journal of Physical Chemistry B
  • Biophysical Journal
  • arXiv (Cornell University)
  • Journal of Medicinal Chemistry
  • PLoS Computational Biology

Best Publications

  • CHARMM-GUI Input Generator for NAMD, Gromacs, Amber, Openmm, and CHARMM/OpenMM Simulations using the CHARMM36 Additive Force Field

    Jumin Lee;Xi Cheng;Jason M. Swails;Min Sun Yeom

  • OpenMM 7: Rapid development of high performance algorithms for molecular dynamics.

    Peter Eastman;Jason Swails;John D. Chodera;Robert T. McGibbon

  • MoleculeNet: a benchmark for molecular machine learning

    Zhenqin Wu;Bharath Ramsundar;Evan N. Feinberg;Joseph Gomes

  • MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories

    Robert T. McGibbon;Kyle A. Beauchamp;Matthew P. Harrigan;Christoph Klein

  • Molecular graph convolutions: moving beyond fingerprints

    Steven M. Kearnes;Kevin McCloskey;Marc Berndl;Vijay S. Pande

  • Current Status of the AMOEBA Polarizable Force Field

    Jay W. Ponder;Chuanjie Wu;Pengyu Ren;Vijay S. Pande

  • Markov State Models: From an Art to a Science

    Brooke E. Husic;Vijay S. Pande

  • Low Data Drug Discovery with One-Shot Learning

    Han Altae-Tran;Bharath Ramsundar;Aneesh S. Pappu;Vijay S. Pande

  • Random-coil behavior and the dimensions of chemically unfolded proteins

    Jonathan E. Kohn;Ian S. Millett;Jaby Jacob;Jaby Jacob;Bojan Zagrovic

  • Absolute comparison of simulated and experimental protein-folding dynamics

    Christopher D. Snow;Houbi Nguyen;Vijay S. Pande;Martin Gruebele

  • Exploring the Helix-Coil Transition via All-Atom Equilibrium Ensemble Simulations

    Eric J. Sorin;Vijay S. Pande

  • Screen Savers of the World Unite

    Michael Shirts;Vijay S. Pande

  • Everything you wanted to know about Markov State Models but were afraid to ask.

    Vijay S. Pande;Kyle Beauchamp;Gregory R. Bowman

  • OpenMM 4: A reusable, extensible, hardware independent library for high performance molecular simulation

    Peter Eastman;Mark S. Friedrichs;John D. Chodera;Randall J. Radmer

  • Extremely precise free energy calculations of amino acid side chain analogs: Comparison of common molecular mechanics force fields for proteins

    Michael R. Shirts;Jed W. Pitera;William C. Swope;Vijay S. Pande

  • Automatic discovery of metastable states for the construction of Markov models of macromolecular conformational dynamics.

    John D. Chodera;Nina Singhal;Vijay S. Pande;Ken A. Dill

  • Accelerating Molecular Dynamic Simulation on Graphics Processing Units

    Mark S. Friedrichs;Peter Eastman;Vishal Vaidyanathan;Mike Houston

  • Improvements in Markov State Model Construction Reveal Many Non-Native Interactions in the Folding of NTL9

    Christian R. Schwantes;Vijay S. Pande

  • Graph convolutional policy network for goal-directed molecular graph generation

    Jiaxuan You;Bowen Liu;Rex Ying;Vijay Pande

  • Alchemical free energy methods for drug discovery: progress and challenges

    John D Chodera;David L Mobley;Michael R Shirts;Richard W Dixon

  • Molecular Simulation of ab Initio Protein Folding for a Millisecond Folder NTL9(1-39)

    Vincent A. Voelz;Gregory R. Bowman;Kyle Beauchamp;Vijay S. Pande

  • An Introduction to Markov State Models and Their Application to Long Timescale Molecular Simulation

    Gregory R. Bowman;Vijay S. Pande;Frank Noé

  • On the transition coordinate for protein folding

    Rose Du;Vijay S. Pande;Vijay S. Pande;Alexander Yu. Grosberg;Toyoichi Tanaka

Frequent Co-Authors

Alexander Y. Grosberg
Alexander Y. Grosberg New York University
John D. Chodera
John D. Chodera Memorial Sloan Kettering Cancer Center
Xuhui Huang
Xuhui Huang University of Wisconsin–Madison
Teresa Head-Gordon
Teresa Head-Gordon University of California, Berkeley
Russ B. Altman
Russ B. Altman Stanford University
Axel T. Brunger
Axel T. Brunger Stanford University
Sebastian Doniach
Sebastian Doniach Stanford University
Todd J. Martínez
Todd J. Martínez Stanford University
Daniel S. Rokhsar
Daniel S. Rokhsar University of California, Berkeley

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