Author

V. S. Pande

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Biophysics· 7

Signature Assays, Organisms & Methods

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Research Focus:protein folding & dynamics· 4 Approach:statistical model· 4 Approach:deep learning· 3 Assay:protein structure· 2 Research Focus:software / tool· 2 Assay:structural biology· 2 Approach:Bayesian inference· 1 Approach:biophysical modeling· 1

Frequent Co-Authors

K. A. McKiernan· 3 shared M. P. Harrigan· 3 shared B. E. Husic· 2 shared J. D. Chodera· 2 shared K. A. Beauchamp· 2 shared M. M. Sultan· 2 shared P. Eastman· 2 shared R. A. Denny· 2 shared

Activity by Year

2016-2019 · peak 3/yr

Co-Author Collaboration Network

10 top collaborators · 29 mutual co-author links

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3 shared papersBiophysics

K. A. McKiernan

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Author profile →

7 papers

Recent·Most cited

Dynamical model of the CLC-2 ion channel reveals conformational changes associated with selectivity-filter gating

K. A. McKiernan, A. K. Koster, M. Maduke, V. S. Pande

This paper uses molecular dynamics simulations to model CLC-2 ion channel conformational changes, revealing how GLUex protonation affects gate opening and selectivity-filter gating.

bioRxiv · Dec 1, 2019Biophysics

Bayesian analysis of isothermal titration calorimetry for binding thermodynamics

T. H. Nguyen, A. S. Rustenburg, S. G. Krimmer, H. Zhang, J. D. Clark, P. A. Novick, K. Branson, V. S. Pande, J. D. Chodera, D. D. L. Minh

This paper introduces a Bayesian framework for analyzing ITC data to better estimate thermodynamic parameters and their uncertainties.

bioRxiv · May 21, 2018Biophysics

Modeling the Mechanism of CLN025Beta-Hairpin Formation

K. A. McKiernan, B. E. Husic, V. S. Pande

The paper simulates CLN025 beta-hairpin folding using force fields to analyze thermodynamics, kinetics, and mechanism, finding hydrogen bond formation in the turn region is rate-limiting.

bioRxiv · Aug 25, 2017Biophysics

OpenMM 7: Rapid Development of High Performance Algorithms for Molecular Dynamics

P. Eastman, J. Swails, J. D. Chodera, R. T. McGibbon, Y. Zhao, K. A. Beauchamp, L.-P. Wang, A. C. Simmonett, M. P. Harrigan, C. D. Stern, R. P. Wiewiora, B. R. Brooks, V. S. Pande

OpenMM 7 enables rapid development of high-performance molecular dynamics algorithms with extensible features that work across hardware types without modifying the core toolkit.

bioRxiv · Jun 28, 2017Biophysics

Millisecond Dynamics Of BTK Reveal Kinome-Wide Conformational Plasticity Within The Apo Kinase Domain

M. M. Sultan, R. A. Denny, R. Unwalla, F. Lovering, V. S. Pande

This study uses molecular dynamics and Markov state models to analyze BTK's conformational dynamics, revealing new druggable states and the role of protonation in modulating its activity.

bioRxiv · May 9, 2017Biophysics

Markov modeling reveals novel intracellular modulation of the human TREK-2 selectivity filter

M. P. Harrigan, K. A. McKiernan, V. Shanmugasundaram, R. A. Denny, V. S. Pande

The paper uses molecular dynamics simulations and Markov modeling to show that membrane stretch induces a novel 'pinched' state in the TREK-2 channel's selectivity filter, impairing ion conduction.

bioRxiv · Dec 7, 2016Biophysics

MSMBuilder: Statistical Models for Biomolecular Dynamics

M. P. Harrigan, M. M. Sultan, C. X. Hernandez, B. E. Husic, P. Eastman, C. R. Schwantes, K. A. Beauchamp, R. T. McGibbon, V. S. Pande

MSMBuilder is a software package for building statistical models of high-dimensional time-series data, particularly for biomolecular dynamics, using methods like Markov State Models and HMMs.

bioRxiv · Oct 30, 2016Biophysics