Search filters

List of works by Vijay Pande

"Cross-graining": efficient multi-scale simulation via Markov state models.

scientific article published in January 2010

A Simple Model Predicts Experimental Folding Rates and a Hub-Like Topology ⬇️

scientific article (publication date: 14 June 2012)

A bundling of viral fusion mechanisms

scientific article

A minimum variance clustering approach produces robust and interpretable coarse-grained models.

scientific article published on 18 December 2017

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

scientific article (publication date: 18 March 2014)

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

scientific article

A new set of molecular mechanics parameters for hydroxyproline and its use in molecular dynamics simulations of collagen-like peptides

scientific article

A role for confined water in chaperonin function

scientific article published on 19 August 2008

Absolute comparison of simulated and experimental protein-folding dynamics

scientific article

Accelerated Molecular Dynamics Simulations with the AMOEBA Polarizable Force Field on Graphics Processing Units

scientific article

Accelerating molecular dynamic simulation on graphics processing units

scientific article

Accurate and efficient corrections for missing dispersion interactions in molecular simulations

scientific article published on 19 October 2007

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

scientific article published on 3 March 2014

Adaptive Seeding: A New Method for Simulating Biologically Relevant Timescales

Advanced Potential Energy Surfaces for Molecular Simulation

scientific article published on 11 August 2016

Alchemical free energy methods for drug discovery: progress and challenges

scientific article

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

scientific article

Assessment of the protein-structure refinement category in CASP8

scientific article

Atomic-resolution simulations predict a transition state for vesicle fusion defined by contact of a few lipid tails

scientific article

Atomistic folding simulations of the five-helix bundle protein λ(6−85).

scientific article

Atomistic protein folding simulations on the submillisecond time scale using worldwide distributed computing

scientific article

Automated Discovery and Refinement of Reactive Molecular Dynamics Pathways

scientific article published on 18 December 2015

Automated design of collective variables using supervised machine learning

scientific article published on 01 September 2018

Automatic Selection of Order Parameters in the Analysis of Large Scale Molecular Dynamics Simulations.

scientific article

Automatic discovery of metastable states for the construction of Markov models of macromolecular conformational dynamics

scientific article published in April 2007

Bayesian analysis of isothermal titration calorimetry for binding thermodynamics

scientific article published in PLoS ONE

Bayesian comparison of Markov models of molecular dynamics with detailed balance constraint

scientific article published in July 2009

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

scientific article published in January 2010

Bayesian energy landscape tilting: towards concordant models of molecular ensembles

scientific article published on March 2014

Bayesian inference for Brownian dynamics ⬇️

scientific article published on July 19, 2010

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

scientific article

Bayesian update method for adaptive weighted sampling

scientific article

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

scientific article published on 16 May 2014

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

scientific article published on 17 March 2017

CAMPAIGN: an open-source library of GPU-accelerated data clustering algorithms ⬇️

scientific article published on June 27, 2011

CCMA: A Robust, Parallelizable Constraint Method for Molecular Simulations

scientific article published on February 2010

CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field

scientific article

Calculation of rate spectra from noisy time series data.

scientific article

Calculations of the electric fields in liquid solutions

scientific article published on 10 December 2013

Characterization and Rapid Sampling of Protein Folding Markov State Model Topologies ⬇️

scientific article published on October 11, 2011

Chemical denaturants inhibit the onset of dewetting

scientific article published on 16 August 2008

Choosing weights for simulated tempering

scientific article published on 16 July 2007

Cloud computing approaches for prediction of ligand binding poses and pathways.

scientific article

Cloud-based simulations on Google Exacycle reveal ligand modulation of GPCR activation pathways

scientific article published on 15 December 2013

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

scientific article

Combining mutual information with structural analysis to screen for functionally important residues in influenza hemagglutinin

scientific article

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

scientific article published on 27 December 2008

Comparison of efficiency and bias of free energies computed by exponential averaging, the Bennett acceptance ratio, and thermodynamic integration

scientific article

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

scientific article

Computational Modeling of β-Secretase 1 (BACE-1) Inhibitors Using Ligand Based Approaches.

scientific article

Conformational heterogeneity of the calmodulin binding interface.

scientific article published on 4 April 2016

Conserve Water: A Method for the Analysis of Solvent in Molecular Dynamics.

scientific article published in March 2015

Control of membrane fusion mechanism by lipid composition: predictions from ensemble molecular dynamics

scientific article

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

scientific article

Copernicus

Corrigendum: Cloud-based simulations on Google Exacycle reveal ligand modulation of GPCR activation pathways

scientific article published on 01 September 2015

Corrigendum: Conformational heterogeneity of the calmodulin binding interface.

scientific article published on 10 August 2016

Current status of the AMOEBA polarizable force field

scientific article

Derivation and assessment of phase-shifted, disordered vector field models for frustrated solvent interactions ⬇️

scientific article published on February 28, 2013

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

scientific article

Direct calculation of the binding free energies of FKBP ligands

scientific article published on August 2005

Discovering chemistry with an ab initio nanoreactor

scientific article

Discovery of a regioselectivity switch in nitrating P450s guided by molecular dynamics simulations and Markov models

scientific article published on 21 March 2016

Discovery of novel brain permeable and G protein-biased beta-1 adrenergic receptor partial agonists for the treatment of neurocognitive disorders

scientific article published on 26 July 2017

Does native state topology determine the RNA folding mechanism?

scientific article published in April 2004

Does water play a structural role in the folding of small nucleic acids?

scientific article

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

scientific article published on 30 March 2020

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

scientific article published on August 2014

Dynamical reweighting: improved estimates of dynamical properties from simulations at multiple temperatures

scientific article

Effects of familial mutations on the monomer structure of Aβ₄₂.

scientific article published on 18 December 2012

Efficient gaussian density formulation of volume and surface areas of macromolecules on graphical processing units

scientific article

Efficient maximum likelihood parameterization of continuous-time Markov processes

scientific article published in July 2015

Efficient nonbonded interactions for molecular dynamics on a graphics processing unit

scientific article

Eigenvalues of the homogeneous finite linear one step master equation: Applications to downhill folding ⬇️

scientific article published on December 7, 2012

Electric fields at the active site of an enzyme: direct comparison of experiment with theory.

scientific article published on July 2006

Elucidating Ligand-Modulated Conformational Landscape of GPCRs Using Cloud-Computing Approaches

scientific article published on 24 March 2015

Emergence of Glass-like Behavior in Markov State Models of Protein Folding Dynamics ⬇️

scientific article published on April 3, 2013

Empirical force-field assessment: The interplay between backbone torsions and noncovalent term scaling

scientific article

Engineering a Single-Agent Cytokine/Antibody Fusion That Selectively Expands Regulatory T Cells for Autoimmune Disease Therapy

scientific article published on 13 August 2018

Enhanced Modeling via Network Theory: Adaptive Sampling of Markov State Models ⬇️

scientific article published on January 1, 2010

Ensemble molecular dynamics yields submillisecond kinetics and intermediates of membrane fusion

scholarly article

Entropy-production-driven oscillators in simple nonequilibrium networks

scientific article published on 24 March 2015

Equilibrium Free Energies from Nonequilibrium Measurements Using Maximum-Likelihood Methods ⬇️

scientific article published on 02 October 2003

Erratum: Corrigendum: Discovering chemistry with an ab initio nanoreactor

scientific article published on 17 December 2014

Error analysis and efficient sampling in Markovian state models for molecular dynamics

scientific article published in November 2005

Everything you wanted to know about Markov State Models but were afraid to ask

scientific article

Exploring the helix-coil transition via all-atom equilibrium ensemble simulations

scientific article

Extremely precise free energy calculations of amino acid side chain analogs: Comparison of common molecular mechanics force fields for proteins

article

Finding Our Way in the Dark Proteome

scientific article published on 07 July 2016

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

scientific article

Foldamer dynamics expressed via Markov state models. II. State space decomposition

scientific article

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

scientific article published in December 2004

Folding and misfolding of the collagen triple helix: Markov analysis of molecular dynamics simulations

scientific article

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

scientific article published on 01 April 2004

Folding@home

volunteer computing project simulating protein folding

Folding@home: Lessons from eight years of volunteer distributed computing

article published in 2009

Functional understanding of solvent structure in GroEL cavity through dipole field analysis ⬇️

scientific article published on April 28, 2013

Heat dissipation guides activation in signaling proteins

scientific article

Heterogeneity even at the speed limit of folding: large-scale molecular dynamics study of a fast-folding variant of the villin headpiece

scientific article

How does averaging affect protein structure comparison on the ensemble level?

scientific article

How well can simulation predict protein folding kinetics and thermodynamics?

scientific article

Identification of simple reaction coordinates from complex dynamics. ⬇️

scientific article published in January 2017

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

scientific article published on April 9, 2013

Inclusion of persistence length-based secondary structure in replica field theoretic models of heteropolymer freezing

scientific article published on September 2013

Increased detection of structural templates using alignments of designed sequences ⬇️

scientific article published on May 15, 2003

Inferring the rate-length law of protein folding

scientific article

Inside the chaperonin toolbox: theoretical and computational models for chaperonin mechanism

scientific article published on 10 February 2009

Insights into nucleic acid conformational dynamics from massively parallel stochastic simulations

scientific article

Introduction and overview of this book

scientific article published in January 2014

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

scientific article published on January 2012

Kinetic computational alanine scanning: application to p53 oligomerization

scientific article

Kinetic definition of protein folding transition state ensembles and reaction coordinates

scientific article published on 14 April 2006

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

scientific article published on 6 June 2013

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

scientific article

Local structure formation in simulations of two small proteins

scientific article published on 11 October 2006

Low Data Drug Discovery with One-Shot Learning

scientific article

MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories.

scientific article published in October 2015

MSMBuilder2: Modeling Conformational Dynamics on the Picosecond to Millisecond Scale ⬇️

scientific article published on October 11, 2011

MSMBuilder: Statistical Models for Biomolecular Dynamics.

scientific article

Marked difference in saxitoxin and tetrodotoxin affinity for the human nociceptive voltage-gated sodium channel (Nav1.7) [corrected]

scientific article

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

scientific article published on April 2016

Markov State Models: From an Art to a Science.

scientific article

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

scientific article

Markov state model reveals folding and functional dynamics in ultra-long MD trajectories

scientific article

Markov state models provide insights into dynamic modulation of protein function

scientific article

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

scientific article

Modeling molecular kinetics with tICA and the kernel trick

scientific article

Modeling the mechanism of CLN025 beta-hairpin formation

scientific article

Molecular Dynamics Simulations for the Ranking, Evaluation, and Refinement of Computationally Designed Proteins ⬇️

scientific article published on January 1, 2013

Molecular dynamics simulation of lipid reorientation at bilayer edges.

scientific article

Molecular simulation of ab initio protein folding for a millisecond folder NTL9(1-39)

scientific article

Molecular simulation of multistate peptide dynamics: a comparison between microsecond timescale sampling and multiple shorter trajectories

scientific article published in August 2008

MoleculeNet: a benchmark for molecular machine learning.

scientific article published on 31 October 2017

Multiplexed-replica exchange molecular dynamics method for protein folding simulation

scientific article

Nanotube confinement denatures protein helices.

scientific article

Native-like mean structure in the unfolded ensemble of small proteins

scientific article published on October 2002

Non-bulk-like solvent behavior in the ribosome exit tunnel

scientific article

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

scientific article published in November 2017

Note: Variational encoding of protein dynamics benefits from maximizing latent autocorrelation

scientific article published on 01 December 2018

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

scientific article published in April 2005

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

scientific article

OpenMM 7: Rapid development of high performance algorithms for molecular dynamics.

scientific article

OpenMM: A Hardware Independent Framework for Molecular Simulations

scientific article published on July 2015

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

scientific article published on June 28, 2011

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

scientific article published on November 2016

PAPER--accelerating parallel evaluations of ROCS.

scientific article published in January 2010

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

scientific article

Percolation-like phase transitions in network models of protein dynamics

scientific article published on June 2015

Persistent Topology and Metastable State in Conformational Dynamics ⬇️

scientific article published on April 2, 2013

Persistent voids: a new structural metric for membrane fusion.

scientific article

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

scientific article published on 01 November 2018

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

scientific article published on 9 March 2011

Polarizable atomic multipole X-ray refinement: application to peptide crystals

scientific article published on 14 August 2009

Polarizable atomic multipole x-ray refinement: hydration geometry and application to macromolecules

scientific article

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

scientific article published on June 2015

PotentialNet for Molecular Property Prediction

scientific article published on 02 November 2018

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

scientific article published on 24 January 2008

Predicting structure and dynamics of loosely-ordered protein complexes: influenza hemagglutinin fusion peptide.

scientific article

Probing the origins of two-state folding

scientific article published on October 2013

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

scientific article published on September 2009

Protein Folding Is Mechanistically Robust ⬇️

scientific article published on February 21, 2012

Protein folded states are kinetic hubs

scientific article

Protein folding under confinement: a role for solvent

scholarly article

Quantitative comparison of villin headpiece subdomain simulations and triplet-triplet energy transfer experiments

scientific article

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

scientific article published in April 2002

Rapid equilibrium sampling initiated from nonequilibrium data

scientific article

Rationally designed turn promoting mutation in the amyloid-β peptide sequence stabilizes oligomers in solution

scientific article

Rattling the cage: computational models of chaperonin-mediated protein folding

scientific article published on 04 March 2008

Reintroducing Electrostatics into Macromolecular Crystallographic Refinement: Application to Neutron Crystallography and DNA Hydration

scientific article

Revised Parameters for the AMOEBA Polarizable Atomic Multipole Water Model

scientific article published on 26 February 2015

Rings of Power

1992 video game

SWEETLEAD: an in silico database of approved drugs, regulated chemicals, and herbal isolates for computer-aided drug discovery

scientific article (publication date: 2013)

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

scientific article

Side-chain recognition and gating in the ribosome exit tunnel.

scientific article

Simbios: an NIH national center for physics-based simulation of biological structures

scientific article published on 10 November 2011

Simple few-state models reveal hidden complexity in protein folding ⬇️

scientific article published on July 9, 2012

Simulated tempering yields insight into the low-resolution Rosetta scoring functions

scientific article

Simulated unfolded-state ensemble and the experimental NMR structures of villin headpiece yield similar wide-angle solution X-ray scattering profiles

scientific article published on 01 September 2006

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

scientific article

Simulation of folding of a small alpha-helical protein in atomistic detail using worldwide-distributed computing

scientific article

Simulations of the role of water in the protein-folding mechanism

scientific article

Slow unfolded-state structuring in Acyl-CoA binding protein folding revealed by simulation and experiment

scientific article (publication date: August 2012)

Solvation free energies of amino acid side chain analogs for common molecular mechanics water models

scientific article published in April 2005

Solvent viscosity dependence of the folding rate of a small protein: distributed computing study

scientific article (publication date: September 2003)

Solvent viscosity dependence of the protein folding dynamics

scientific article published on 30 January 2008

Solving the RNA design problem with reinforcement learning.

scientific article published on 21 June 2018

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

scientific article

Statistical model selection for Markov models of biomolecular dynamics

scientific article published on 25 April 2014

Structural basis for influence of viral glycans on ligand binding by influenza hemagglutinin.

scientific article

Systematic improvement of a classical molecular model of water

scientific article published on 14 August 2013

Taming the complexity of protein folding ⬇️

scientific article published on February 1, 2011

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

scientific article published on April 2009

The Simbios National Center: Systems Biology in Motion

scientific article

The Trp cage: folding kinetics and unfolded state topology via molecular dynamics simulations

scientific article published on December 2002

The roles of entropy and kinetics in structure prediction

scientific article

The social network (of protein conformations)

scientific article

The solvation interface is a determining factor in peptide conformational preferences

scientific article published on 05 December 2005

Theory for an order-driven disruption of the liquid state in water

scientific article published in January 2008

Thoroughly sampling sequence space: large-scale protein design of structural ensembles

scientific article

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

scientific article published on 10 December 2012

Towards simple kinetic models of functional dynamics for a kinase subfamily

scientific article published on 09 July 2018

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

scientific article published on 27 October 2016

Transfer Learning from Markov Models Leads to Efficient Sampling of Related Systems.

scientific article published on 22 September 2017

Transferable neural networks for enhanced sampling of protein dynamics

scientific article published on 12 March 2018

Transition path theory analysis of c-Src kinase activation

scientific article published on August 2016

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

scholarly article

Tungstate as a Transition State Analog for Catalysis by Alkaline Phosphatase

scientific article

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

scientific article

United polarizable multipole water model for molecular mechanics simulation ⬇️

scientific article published in July 2015

Using massively parallel simulation and Markovian models to study protein folding: examining the dynamics of the villin headpiece

scientific article (publication date: 28 April 2006)

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

scientific article published on July 2004

Validation of Markov state models using Shannon's entropy.

scientific article published in February 2006

Variational cross-validation of slow dynamical modes in molecular kinetics ⬇️

scientific article

Variational encoding of complex dynamics

scientific article published on 01 June 2018

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

scientific article published on 14 February 2017

Water ordering at membrane interfaces controls fusion dynamics

scientific article

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

scientific article published on 6 April 2017

Paulina is supported by:

About Paulina

Help