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
•Journal Article
A Simple Model Predicts Experimental Folding Rates and a Hub-Like Topology
Thomas J. Lane,Vijay S. Pande +1 more
TL;DR: A simple model is presented that describes general features of protein folding, in good agreement with experimental results and detailed all-atom simulations, including the scaling of τ(f) with N, two-state thermodynamics, a sharp peak in C(V), and native-state fluctuations.
3
Towards simple kinetic models of functional dynamics for a kinase subfamily
TL;DR: The findings indicate that in the absence of their regulatory partners, SFK members have similar in-silico dynamics with active state populations ranging from 4-40% and activation timescales in the hundreds of microseconds, and establish the utility of MSMs for studying protein families.
Dynamical model of the CLC-2 ion channel exhibits a two-step gating mechanism
TL;DR: A Markov state model of the conformational dynamics involved in regulating the inner and outer gates of the CLC-2 ion channel suggests a new mechanism for channel activation and highlights a dominant pathway between a highly stable closed state and several new protein conformations not observed in any previously elucidated CLC structure.
3
Application of new informatics tools for identifying allosteric lead ligands of the c-Src kinase
TL;DR: A novel lead enrichment protocol is developed using new target and lead enrichment software to identify sixteen allosteric lead ligands of the c-Src kinase, recommended for further experimental testing for the existence of theallosteric pocket in Src.
Corrigendum: Conformational heterogeneity of the calmodulin binding interface.
TL;DR: In the Methods sections ‘Simulation details for apo CaM' and ‘ Simpson details for holoCaM,' the aggregate simulation times for each data set were inadvertently swapped, and the correct aggregate simulation speeds are 256 and 455 μs, respectively.