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
Cloud-based simulations on Google Exacycle reveal ligand modulation of GPCR activation pathways
Kai Kohlhoff,Diwakar Shukla,Morgan Lawrenz,Gregory R. Bowman,David E. Konerding,Dan Belov,Russ B. Altman,Vijay S. Pande +7 more
TL;DR: This work used Google's Exacycle cloud computing platform to simulate 2 milliseconds of dynamics of the β2 adrenergic receptor — a major drug target G protein-coupled receptor (GPCR) and provides an atomistic description of the activation of a GPCR, revealing multiple activation pathways.
Using generalized ensemble simulations and Markov state models to identify conformational states.
TL;DR: The use of the MSMBuilder package is described to build Markov State Models (MSMs) to identify the metastable states from Generalized Ensemble simulations, as well as other simulation datasets.
Heterogeneity Even at the Speed Limit of Folding: Large-scale Molecular Dynamics Study of a Fast-folding Variant of the Villin Headpiece
TL;DR: Large-scale molecular dynamics simulations on a set of nine unfolded conformations of the fastest-folding protein yet discovered, a variant of the villin headpiece subdomain, reveal kinetic complexity not resolved in the experimental data.
Bayesian Energy Landscape Tilting: Towards Concordant Models of Molecular Ensembles
TL;DR: BELT's principled framework enables practical predictions for complex biomolecular systems from discordant simulations and sparse data, and recovers set-aside measurements not used in the fitting and report accurate errors, even when starting from highly inaccurate simulations.