Vijay S Pande

发表

Potential-based dynamical reweighting for Markov state models of protein dynamics.

Jeffrey K Weber, Vijay S Pande, V. Pande, 2015, Journal of chemical theory and computation.

Protein folding is mechanistically robust.

Jeffrey K Weber, Vijay S Pande, V. Pande, 2012, Biophysical journal.

To milliseconds and beyond: challenges in the simulation of protein folding.

Diwakar Shukla, Thomas J Lane, Vijay S Pande, 2013, Current opinion in structural biology.

Progress and challenges in the automated construction of Markov state models for full protein systems.

Vijay S Pande, Kyle A Beauchamp, Gregory R Bowman, 2009, The Journal of chemical physics.

CCMA: A Robust, Parallelizable Constraint Method for Molecular Simulations.

Vijay S Pande, Peter Eastman, V. Pande, 2010, Journal of chemical theory and computation.

MSMBuilder: Statistical Models for Biomolecular Dynamics

Mohammad M. Sultan, Vijay S Pande, Carlos X. Hernández, 2016, bioRxiv.

Using path sampling to build better Markovian state models: predicting the folding rate and mechanism of a tryptophan zipper beta hairpin.

Vijay S Pande, Christopher D Snow, Nina Singhal, 2004, The Journal of chemical physics.

Enhanced modeling via network theory: Adaptive sampling of Markov state models.

Vijay S Pande, Gregory R Bowman, Daniel L Ensign, 2010, Journal of chemical theory and computation.

Are Protein Force Fields Getting Better? A Systematic Benchmark on 524 Diverse NMR Measurements.

Rhiju Das, Vijay S Pande, Kyle A Beauchamp, 2012, Journal of chemical theory and computation.

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

Vijay S Pande, Christian R Schwantes, V. Pande, 2013, Journal of chemical theory and computation.

Thoroughly sampling sequence space: Large‐scale protein design of structural ensembles

Vijay S Pande, Stefan M. Larson, Jeremy L. England, 2002, Protein science : a publication of the Protein Society.

MDTraj: a modern, open library for the analysis of molecular dynamics trajectories

Thomas J Lane, Vijay S Pande, Carlos X. Hernández, 2014, bioRxiv.

Optimized parameter selection reveals trends in Markov state models for protein folding.

Mohammad M. Sultan, Vijay S Pande, Mohammad M Sultan, 2016, The Journal of chemical physics.

Characterization and rapid sampling of protein folding Markov state model topologies.

Jeffrey K Weber, Vijay S Pande, V. Pande, 2011, Journal of chemical theory and computation.

Molecular dynamics simulations for the ranking, evaluation, and refinement of computationally designed proteins.

Vijay S Pande, Gert Kiss, K N Houk, 2013, Methods in enzymology.

Communication: Adaptive boundaries in multiscale simulations.

Vijay S Pande, Jason A Wagoner, 2018, The Journal of chemical physics.

K-Means for Parallel Architectures Using All-Prefix-Sum Sorting and Updating Steps

Vijay S Pande, Russ B Altman, Kai J Kohlhoff, 2013, IEEE Transactions on Parallel and Distributed Systems.

OpenMM 4: A Reusable, Extensible, Hardware Independent Library for High Performance Molecular Simulation.

Diwakar Shukla, Mike Houston, Thomas J Lane, 2013, Journal of chemical theory and computation.

Calculation of rate spectra from noisy time series data

Vincent A Voelz, Vijay S Pande, 2012, Proteins.

Automated design of collective variables using supervised machine learning.

Mohammad M. Sultan, Vijay S Pande, Mohammad M Sultan, 2018, The Journal of chemical physics.

Theoretical restrictions on longest implicit time scales in Markov state models of biomolecular dynamics.

Vijay S Pande, Anton V. Sinitskiy, Anton V Sinitskiy, 2017, The Journal of chemical physics.

Bayesian Energy Landscape Tilting: Towards Concordant Models of Molecular Ensembles

Rhiju Das, Vijay S Pande, Kyle A Beauchamp, 2014, bioRxiv.

Long Timestep Molecular Dynamics on the Graphical Processing Unit.

Vijay S Pande, Christopher R Sweet, James C Sweet, 2013, Journal of chemical theory and computation.

Variational encoding of complex dynamics.

Mohammad M. Sultan, Vijay S Pande, Carlos X. Hernández, 2017, Physical review. E.

Convergence of folding free energy landscapes via application of enhanced sampling methods in a distributed computing environment.

Vijay S Pande, Gregory R Bowman, Xuhui Huang, 2008, The Journal of chemical physics.

Ward Clustering Improves Cross-Validated Markov State Models of Protein Folding.

Vijay S Pande, Brooke E Husic, V. Pande, 2017, Journal of chemical theory and computation.

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

David L Mobley, Kim Branson, Michael R Shirts, 2011, Current opinion in structural biology.

MSMBuilder2: Modeling Conformational Dynamics at the Picosecond to Millisecond Scale.

Thomas J Lane, Vijay S Pande, Lutz Maibaum, 2011, Journal of chemical theory and computation.

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

Vijay S Pande, Merritt Maduke, Keri A McKiernan, 2020, PLoS Comput. Biol..

Learning Kinetic Distance Metrics for Markov State Models of Protein Conformational Dynamics.

Vijay S Pande, Robert T McGibbon, R. McGibbon, 2013, Journal of chemical theory and computation.

tICA-Metadynamics: Accelerating Metadynamics by Using Kinetically Selected Collective Variables.

Vijay S Pande, Mohammad M Sultan, V. Pande, 2017, Journal of chemical theory and computation.

Identification of simple reaction coordinates from complex dynamics.

Vijay S Pande, Brooke E Husic, Robert T McGibbon, 2016, The Journal of chemical physics.

Efficient maximum likelihood parameterization of continuous-time Markov processes.

Vijay S Pande, Robert T McGibbon, R. McGibbon, 2015, The Journal of chemical physics.

Bayesian update method for adaptive weighted sampling.

Vijay S Pande, Daniel L Ensign, Sanghyun Park, 2006, Physical review. E, Statistical, nonlinear, and soft matter physics.

Taming the complexity of protein folding.

Vincent A Voelz, Vijay S Pande, Gregory R Bowman, 2011, Current opinion in structural biology.

Advanced Potential Energy Surfaces for Molecular Simulation.

Jonathan W Essex, Qiao Zeng, Jay W Ponder, 2016, The journal of physical chemistry. B.

The social network (of protein conformations)

Vijay S Pande, John D Chodera, V. Pande, 2011, Proceedings of the National Academy of Sciences.

Using generalized ensemble simulations and Markov state models to identify conformational states.

Xuhui Huang, Vijay S Pande, Gregory R Bowman, 2009, Methods.

A Minimum Variance Clustering Approach Produces Robust and Interpretable Coarse-Grained Models.

Mohammad M. Sultan, Vijay S Pande, Mohammad M Sultan, 2017, Journal of chemical theory and computation.

Perspective: Computational chemistry software and its advancement as illustrated through three grand challenge cases for molecular science.

Cecilia Clementi, Daniel G A Smith, T Daniel Crawford, 2018, The Journal of chemical physics.

The predicted structure of the headpiece of the Huntingtin protein and its implications on Huntingtin aggregation.

Xuhui Huang, Vijay S Pande, Judith Frydman, 2009, Journal of molecular biology.

Markov State Models and tICA Reveal a Nonnative Folding Nucleus in Simulations of NuG2.

Diwakar Shukla, Vijay S Pande, Christian R Schwantes, 2016, Biophysical journal.

Folding probabilities: a novel approach to folding transitions and the two-dimensional Ising-model.

Vijay S Pande, Bojan Zagrovic, Jessica Shapiro, 2004, The Journal of chemical physics.

Revised Parameters for the AMOEBA Polarizable Atomic Multipole Water Model.

Jay W Ponder, Vijay S Pande, Teresa Head-Gordon, 2015, The journal of physical chemistry. B.

The Fip35 WW domain folds with structural and mechanistic heterogeneity in molecular dynamics simulations.

Vijay S Pande, Daniel L Ensign, V. Pande, 2009, Biophysical journal.

Calculation of local water densities in biological systems: a comparison of molecular dynamics simulations and the 3D-RISM-KH molecular theory of solvation.

Andriy Kovalenko, Vijay S Pande, David Wishart, 2011, The journal of physical chemistry. B.

Foldamer simulations: novel computational methods and applications to poly-phenylacetylene oligomers.

Vijay S Pande, V. Pande, S. P. Elmer, 2004, The Journal of chemical physics.

Polarizable Atomic Multipole X-Ray Refinement: Particle Mesh Ewald Electrostatics for Macromolecular Crystals.

Vijay S Pande, Michael J Schnieders, Timothy D. Fenn, 2011, Journal of chemical theory and computation.

Complex pathways in folding of protein G explored by simulation and experiment.

Diwakar Shukla, Vijay S Pande, Christian R Schwantes, 2014, Biophysical journal.

Nanotube confinement denatures protein helices.

Vijay S Pande, Eric J. Sorin, V. Pande, 2006, Journal of the American Chemical Society.

Investigating how peptide length and a pathogenic mutation modify the structural ensemble of amyloid beta monomer.

Vijay S Pande, Kyle A Beauchamp, Gregory R Bowman, 2012, Biophysical journal.

Combining molecular dynamics with bayesian analysis to predict and evaluate ligand-binding mutations in influenza hemagglutinin.

Vijay S Pande, Peter M Kasson, Daniel L Ensign, 2009, Journal of the American Chemical Society.

Bayesian detection of intensity changes in single molecule and molecular dynamics trajectories.

Vijay S Pande, Daniel L Ensign, V. Pande, 2010, The journal of physical chemistry. B.

Length dependent folding kinetics of phenylacetylene oligomers: structural characterization of a kinetic trap.

Vijay S Pande, V. Pande, S. P. Elmer, 2005, The Journal of chemical physics.

Local structure formation in simulations of two small proteins.

Vijay S Pande, Guha Jayachandran, Angel E García, 2007, Journal of structural biology.

Sequence optimization for native state stability determines the evolution and folding kinetics of a small protein.

Vijay S Pande, Stefan M Larson, 2003, Journal of molecular biology.

Protein folded states are kinetic hubs

Vijay S Pande, Gregory R Bowman, V. Pande, 2010, Proceedings of the National Academy of Sciences.

Validation of Markov state models using Shannon's entropy.

Vijay S Pande, V. Pande, Sanghyun Park, 2006, The Journal of chemical physics.

Emergence of glass-like behavior in Markov state models of protein folding dynamics.

Jeffrey K Weber, Vijay S Pande, Robert L Jack, 2013, Journal of the American Chemical Society.

Kinetic definition of protein folding transition state ensembles and reaction coordinates.

Vijay S Pande, Christopher D Snow, Young Min Rhee, 2006, Biophysical journal.

(Compressed) sensing and sensibility

Vijay S Pande, 2011, Proceedings of the National Academy of Sciences.

Simple few-state models reveal hidden complexity in protein folding

Vijay S Pande, Kyle A Beauchamp, Kyle A. Beauchamp, 2012, Proceedings of the National Academy of Sciences.

Probing the origins of two-state folding.

Thomas J Lane, Vijay S Pande, Kyle A Beauchamp, 2013, The Journal of chemical physics.

Finite domain simulations with adaptive boundaries: accurate potentials and nonequilibrium movesets.

Vijay S Pande, Jason A Wagoner, Jason A. Wagoner, 2013, The Journal of chemical physics.

One-dimensional reaction coordinate and the corresponding potential of mean force from commitment probability distribution.

Vijay S Pande, Young Min Rhee, V. Pande, 2005, The journal of physical chemistry. B.

Splitting probabilities as a test of reaction coordinate choice in single-molecule experiments.

Vijay S Pande, John D Chodera, V. Pande, 2011, Physical review letters.

Increased detection of structural templates using alignments of designed sequences

Vijay S Pande, Stefan M Larson, John R Desjarlais, 2003, Proteins.

Kinetic computational alanine scanning: application to p53 oligomerization.

Vijay S Pande, William C Swope, Jed W Pitera, 2006, Journal of molecular biology.

Building Force Fields: An Automatic, Systematic, and Reproducible Approach.

Vijay S Pande, Todd J Martinez, Lee-Ping Wang, 2014, The journal of physical chemistry letters.

Parallelized-over-parts computation of absolute binding free energy with docking and molecular dynamics.

Michael R Shirts, Michael R. Shirts, Vijay S Pande, 2006, The Journal of chemical physics.

Dynamical phase transitions reveal amyloid-like states on protein folding landscapes.

Jeffrey K Weber, Vijay S Pande, Christian R Schwantes, 2014, Biophysical journal.

Training and Validation of a Liquid-Crystalline Phospholipid Bilayer Force Field.

Vijay S Pande, Lee-Ping Wang, Keri A McKiernan, 2016, Journal of chemical theory and computation.

Protein folding under confinement: A role for solvent

Vijay S Pande, V. Pande, V. Vishal, 2007, Proceedings of the National Academy of Sciences.

Trp zipper folding kinetics by molecular dynamics and temperature-jump spectroscopy

Vijay S Pande, Christopher D Snow, Linlin Qiu, 2004, Proceedings of the National Academy of Sciences of the United States of America.

A network of molecular switches controls the activation of the two-component response regulator NtrC

Diwakar Shukla, Vijay S Pande, Morgan Lawrenz, 2015, Nature Communications.

Dimerization of the p53 oligomerization domain: identification of a folding nucleus by molecular dynamics simulations.

Vijay S Pande, Christopher D Snow, Young Min Rhee, 2005, Journal of molecular biology.

Bayesian single-exponential kinetics in single-molecule experiments and simulations.

Vijay S Pande, Daniel L Ensign, V. Pande, 2009, The journal of physical chemistry. B.

Optimal use of data in parallel tempering simulations for the construction of discrete-state Markov models of biomolecular dynamics.

Frank Noé, Vijay S Pande, Jan-Hendrik Prinz, 2011, The Journal of chemical physics.

Building a More Predictive Protein Force Field: A Systematic and Reproducible Route to AMBER-FB15.

Joseph Gomes, Vijay S Pande, Kyle A Beauchamp, 2017, The journal of physical chemistry. B.

Finding Our Way in the Dark Proteome.

Vijay S Pande, David H Brookes, Greg L. Hura, 2016, Journal of the American Chemical Society.

Comparison of computational approaches for predicting the effects of missense mutations on p53 function.

Vijay S Pande, William C Swope, Jed W Pitera, 2009, Journal of molecular graphics & modelling.

Solvent viscosity dependence of the protein folding dynamics.

Vijay S Pande, Young Min Rhee, V. Pande, 2008, The journal of physical chemistry. B.

Predicting small-molecule solvation free energies: an informal blind test for computational chemistry.

David L Mobley, Vijay S Pande, Anthony Nicholls, 2008, Journal of medicinal chemistry.

Accurate and efficient corrections for missing dispersion interactions in molecular simulations.

David L Mobley, Michael R Shirts, Michael R. Shirts, 2007, The journal of physical chemistry. B.

Side-chain recognition and gating in the ribosome exit tunnel

Vijay S Pande, Christopher D Snow, V. Pande, 2008, Proceedings of the National Academy of Sciences.

Reintroducing electrostatics into macromolecular crystallographic refinement: application to neutron crystallography and DNA hydration.

Vijay S Pande, Axel T Brunger, Michael J Schnieders, 2011, Structure.

Simulating oligomerization at experimental concentrations and long timescales: A Markov state model approach.

Vijay S Pande, V. Pande, V. Vishal, 2008, The Journal of chemical physics.

A smoothly decoupled particle interface: new methods for coupling explicit and implicit solvent.

Vijay S Pande, Jason A Wagoner, Jason A. Wagoner, 2011, The Journal of chemical physics.

Identification of significantly mutated regions across cancer types highlights a rich landscape of functional molecular alterations

Michael P Snyder, Vijay S Pande, Can Cenik, 2015, Nature Genetics.

RNA simulations: probing hairpin unfolding and the dynamics of a GNRA tetraloop.

Daniel Herschlag, Vijay S Pande, Eric J. Sorin, 2002, Journal of molecular biology.

Activation pathway of Src kinase reveals intermediate states as targets for drug design

Diwakar Shukla, Benoît Roux, Vijay S Pande, 2014 .

A molecular interpretation of 2D IR protein folding experiments with Markov state models.

Vincent A Voelz, Vijay S Pande, Kyle A Beauchamp, 2014, Biophysical journal.

Potential for modulation of the hydrophobic effect inside chaperonins.

Vijay S Pande, Jeremy L. England, Jeremy L England, 2008, Biophysical journal.

Foldamer dynamics expressed via Markov state models. I. Explicit solvent molecular-dynamics simulations in acetonitrile, chloroform, methanol, and water.

Vijay S Pande, V. Pande, S. P. Elmer, 2005, The Journal of chemical physics.

Simple theory of protein folding kinetics.

Vijay S Pande, V. Pande, 2010, Physical review letters.

Unfolded-state dynamics and structure of protein L characterized by simulation and experiment.

Vincent A Voelz, Vijay S Pande, Vincent A. Voelz, 2010, Journal of the American Chemical Society.

Millisecond dynamics of BTK reveal kinome-wide conformational plasticity within the apo kinase domain

Vijay S Pande, Mohammad M Sultan, Frank Lovering, 2017, Scientific Reports.

Statistical model selection for Markov models of biomolecular dynamics.

Vijay S Pande, Christian R Schwantes, Robert T McGibbon, 2014, The journal of physical chemistry. B.

Note: MSM lag time cannot be used for variational model selection.

Vijay S Pande, Brooke E Husic, V. Pande, 2017, The Journal of chemical physics.