Vijay S. Pande
Stanford University
448 Papers
3.6K Citations
Vijay S. Pande is an academic researcher from Stanford University. The author has contributed to research in topics: Protein folding & Computer science. The author has an hindex of 104, co-authored 445 publications. Previous affiliations of Vijay S. Pande include Massachusetts Institute of Technology & Weizmann Institute of Science.
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Papers
Bayesian comparison of Markov models of molecular dynamics with detailed balance constraint
TL;DR: A Bayesian approach is proposed, which makes it possible to differentiate between models at a fixed lag time making use of short trajectories, and applies a conjugate prior for reversible Markov chains.
Calculation of the distribution of eigenvalues and eigenvectors in Markovian state models for molecular dynamics
TL;DR: The uncertainty analysis is extended to derive similar closed-form solutions for the distributions of the eigenvalues and eigenvectors of the transition matrix, quantities that have numerous applications when using the model.
Learning Kinetic Distance Metrics for Markov State Models of Protein Conformational Dynamics.
TL;DR: This work introduces a new approach for learning a distance metric explicitly constructed to model kinetic similarity, which enables the construction of models, especially in the regime of high anisotropy in the diffusion constant, with fewer states than was previously possible.
Network models for molecular kinetics and their initial applications to human health.
TL;DR: The Markov state models, typically built from physical simulations, have already proved useful in understanding human diseases, such as protein misfolding and aggregation in Alzheimer's disease.
Kinetic Definition of Protein Folding Transition State Ensembles and Reaction Coordinates
TL;DR: A method for determining transition states by employing the transmission probability, Ptrans, and which conformations were transition state ensemble members was introduced, providing a framework for a quantitative study of activated relaxation kinetics.