Vijay S. Pande | Academic Influence

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Vijay S. Pande

Chemistry

#571

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#1004

Historical Rank

#265

USA Rank

Cheminformatics

#2

World Rank

#2

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#1

USA Rank

Chemical Engineering

#141

World Rank

#155

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#57

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Organic Chemistry

#244

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#302

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#69

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chemistry Degrees

Vijay S. Pande

Engineering

#1937

World Rank

#2740

Historical Rank

#681

USA Rank

Biomedical Engineering

#86

World Rank

#87

Historical Rank

#15

USA Rank

Applied Physics

#392

World Rank

#408

Historical Rank

#87

USA Rank

engineering Degrees

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Chemistry
Engineering

Vijay S. Pande's Degrees

Bachelors Chemical Engineering University of California, Berkeley

Why Is Vijay S. Pande Influential?

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According to Wikipedia, Vijay Satyanand Pande is a Trinidadian–American scientist and venture capitalist. Pande is the former director of the biophysics program and is best known for orchestrating the distributed computing disease research project known as Folding@home. His research is focused on distributed computing and computer-modelling of microbiology and on improving computer simulations regarding drug-binding, protein design, and synthetic bio-mimetic polymers. Pande became the ninth general partner at venture capital firm Andreessen Horowitz in November 2015. He is the founding investor of their Bio + Health Fund.

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Vijay S. Pande's Published Works

Number of citations in a given year to any of this author's works

Total number of citations to an author for the works they published in a given year. This highlights publication of the most important work(s) by the author

Published Works

CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field (2015) (1867)
MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories. (2015) (1259)
OpenMM 7: Rapid development of high performance algorithms for molecular dynamics (2016) (1117)
Molecular graph convolutions: moving beyond fingerprints (2016) (1103)
Current status of the AMOEBA polarizable force field. (2010) (1023)
MoleculeNet: A Benchmark for Molecular Machine Learning (2017) (931)
Graph Convolutional Policy Network for Goal-Directed Molecular Graph Generation (2018) (642)
Strategies for Pre-training Graph Neural Networks (2019) (621)
Random-coil behavior and the dimensions of chemically unfolded proteins. (2004) (615)
Absolute comparison of simulated and experimental protein-folding dynamics (2002) (609)
Exploring the helix-coil transition via all-atom equilibrium ensemble simulations. (2005) (596)
Extremely precise free energy calculations of amino acid side chain analogs: Comparison of common molecular mechanics force fields for proteins (2003) (561)
Automatic discovery of metastable states for the construction of Markov models of macromolecular conformational dynamics. (2007) (559)
Everything you wanted to know about Markov State Models but were afraid to ask. (2010) (555)
OpenMM 4: A Reusable, Extensible, Hardware Independent Library for High Performance Molecular Simulation. (2013) (530)
Accelerating molecular dynamic simulation on graphics processing units (2009) (524)
MoleculeNet: a benchmark for molecular machine learning† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c7sc02664a (2017) (510)
Low Data Drug Discovery with One-Shot Learning (2016) (504)
Screen Savers of the World Unite! (2000) (490)
Molecular simulation of ab initio protein folding for a millisecond folder NTL9(1-39). (2010) (477)
An Introduction to Markov State Models and Their Application to Long Timescale Molecular Simulation (2014) (468)
Markov State Models: From an Art to a Science. (2018) (451)
On the transition coordinate for protein folding (1998) (449)
Alchemical free energy methods for drug discovery: progress and challenges. (2011) (444)
Improvements in Markov State Model Construction Reveal Many Non-Native Interactions in the Folding of NTL9. (2013) (443)
Massively Multitask Networks for Drug Discovery (2015) (423)
Exploiting a natural conformational switch to engineer an Interleukin-2 superkine (2012) (399)
Are Protein Force Fields Getting Better? A Systematic Benchmark on 524 Diverse NMR Measurements. (2012) (371)
Equilibrium free energies from nonequilibrium measurements using maximum-likelihood methods. (2003) (366)
Cloud-based simulations on Google Exacycle reveal ligand-modulation of GPCR activation pathways (2013) (358)
Solvation free energies of amino acid side chain analogs for common molecular mechanics water models. (2005) (355)
Building Force Fields: An Automatic, Systematic, and Reproducible Approach. (2014) (354)
Progress and challenges in the automated construction of Markov state models for full protein systems. (2009) (350)
MSMBuilder2: Modeling Conformational Dynamics at the Picosecond to Millisecond Scale. (2011) (348)
Comparison of efficiency and bias of free energies computed by exponential averaging, the Bennett acceptance ratio, and thermodynamic integration. (2005) (340)
To milliseconds and beyond: challenges in the simulation of protein folding. (2013) (332)
Atomistic protein folding simulations on the submillisecond time scale using worldwide distributed computing. (2003) (330)
Molecular dynamics simulations of unfolding and refolding of a beta-hairpin fragment of protein G. (1999) (304)
Retrosynthetic Reaction Prediction Using Neural Sequence-to-Sequence Models (2017) (283)
Simulation of folding of a small alpha-helical protein in atomistic detail using worldwide-distributed computing. (2002) (280)
Folding@Home and Genome@Home: Using distributed computing to tackle previously intractable problem (2009) (274)
Using generalized ensemble simulations and Markov state models to identify conformational states. (2009) (269)
Electric Fields at the Active Site of an Enzyme: Direct Comparison of Experiment with Theory (2006) (268)
Systematic improvement of a classical molecular model of water. (2013) (265)
Folding@home: Lessons from eight years of volunteer distributed computing (2009) (262)
Multiplexed-replica exchange molecular dynamics method for protein folding simulation. (2003) (259)
Predicting small-molecule solvation free energies: an informal blind test for computational chemistry. (2008) (256)
Discovering chemistry with an ab initio nanoreactor (2014) (248)
Using path sampling to build better Markovian state models: predicting the folding rate and mechanism of a tryptophan zipper beta hairpin. (2004) (245)
PotentialNet for Molecular Property Prediction (2018) (241)
β-hairpin folding simulations in atomistic detail using an implicit solvent model1 (2001) (240)
MDTraj: a modern, open library for the analysis of molecular dynamics trajectories (2014) (235)
Heteropolymer freezing and design: Towards physical models of protein folding (2000) (233)
Pathways for protein folding: is a new view needed? (1998) (229)
How well can simulation predict protein folding kinetics and thermodynamics? (2005) (225)
The Trp cage: folding kinetics and unfolded state topology via molecular dynamics simulations. (2002) (214)
Protein folded states are kinetic hubs (2010) (212)
Markov State Models Provide Insights into Dynamic Modulation of Protein Function (2015) (211)
MSMBuilder: Statistical Models for Biomolecular Dynamics (2016) (203)
Rapid compaction during RNA folding (2002) (203)
Enhanced modeling via network theory: Adaptive sampling of Markov state models. (2010) (200)
Activation pathway of Src kinase reveals intermediate states as novel targets for drug design (2014) (191)
Is Multitask Deep Learning Practical for Pharma? (2017) (184)
Accurate and efficient corrections for missing dispersion interactions in molecular simulations. (2007) (184)
Building a More Predictive Protein Force Field: A Systematic and Reproducible Route to AMBER-FB15. (2017) (180)
Direct calculation of the binding free energies of FKBP ligands. (2005) (177)
OpenMM: A Hardware-Independent Framework for Molecular Simulations (2010) (177)
Chemical kinetics and mechanisms of complex systems: a perspective on recent theoretical advances. (2014) (177)
Revised Parameters for the AMOEBA Polarizable Atomic Multipole Water Model. (2015) (169)
Heterogeneity even at the speed limit of folding: large-scale molecular dynamics study of a fast-folding variant of the villin headpiece. (2007) (168)
Simulations of the role of water in the protein-folding mechanism. (2004) (168)
Error analysis and efficient sampling in Markovian state models for molecular dynamics. (2005) (164)
Computational Modeling of β-Secretase 1 (BACE-1) Inhibitors Using Ligand Based Approaches (2016) (162)
Trp zipper folding kinetics by molecular dynamics and temperature-jump spectroscopy (2004) (160)
Native-like mean structure in the unfolded ensemble of small proteins. (2002) (159)
Taming the complexity of protein folding. (2011) (159)
Variational cross-validation of slow dynamical modes in molecular kinetics. (2014) (156)
Atomic Convolutional Networks for Predicting Protein-Ligand Binding Affinity (2017) (153)
Using massively parallel simulation and Markovian models to study protein folding: examining the dynamics of the villin headpiece. (2006) (150)
Markov state model reveals folding and functional dynamics in ultra-long MD trajectories. (2011) (147)
Protein folding under confinement: A role for solvent (2007) (143)
Simple few-state models reveal hidden complexity in protein folding (2012) (143)
Solvent viscosity dependence of the folding rate of a small protein: Distributed computing study (2003) (142)
Can conformational change be described by only a few normal modes? (2006) (140)
Slow unfolded-state structuring in Acyl-CoA binding protein folding revealed by simulation and experiment. (2012) (138)
Rapid equilibrium sampling initiated from nonequilibrium data (2009) (134)
Activation pathway of Src kinase reveals intermediate states as targets for drug design (2014) (133)
Atomistic folding simulations of the five-helix bundle protein λ(6−85). (2011) (133)
Efficient nonbonded interactions for molecular dynamics on a graphics processing unit (2010) (130)
Topological methods for exploring low-density states in biomolecular folding pathways. (2008) (129)
Ensemble molecular dynamics yields submillisecond kinetics and intermediates of membrane fusion (2006) (129)
COMPUTING: Screen Savers of the World Unite! (2000) (123)
Variational encoding of complex dynamics. (2017) (122)
Thoroughly sampling sequence space: Large‐scale protein design of structural ensembles (2002) (121)
Control of Membrane Fusion Mechanism by Lipid Composition: Predictions from Ensemble Molecular Dynamics (2007) (114)
tICA-Metadynamics: Accelerating Metadynamics by Using Kinetically Selected Collective Variables. (2017) (113)
Hard Data on Soft Errors: A Large-Scale Assessment of Real-World Error Rates in GPGPU (2009) (112)
Calculation of the distribution of eigenvalues and eigenvectors in Markovian state models for molecular dynamics. (2007) (111)
Finding Our Way in the Dark Proteome. (2016) (110)
Modeling Molecular Kinetics with tICA and the Kernel Trick (2015) (109)
Statistical mechanics of simple models of protein folding and design. (1997) (108)
Unusual compactness of a polyproline type II structure. (2005) (107)
Mechanistic and structural insight into the functional dichotomy between interleukin-2 and interleukin-15 (2012) (106)
Atomic-Resolution Simulations Predict a Transition State for Vesicle Fusion Defined by Contact of a Few Lipid Tails (2010) (104)
Folding pathway of a lattice model for proteins. (1999) (104)
Investigating how peptide length and a pathogenic mutation modify the structural ensemble of amyloid beta monomer. (2012) (103)
RNA simulations: probing hairpin unfolding and the dynamics of a GNRA tetraloop. (2002) (102)
Molecular dynamics simulations reveal ligand-controlled positioning of a peripheral protein complex in membranes (2017) (99)
Mathematical analysis of coupled parallel simulations. (2001) (97)
Deep Learning the Physics of Transport Phenomena (2017) (96)
Nonrandomness in protein sequences: evidence for a physically driven stage of evolution? (1994) (96)
SWEETLEAD: an In Silico Database of Approved Drugs, Regulated Chemicals, and Herbal Isolates for Computer-Aided Drug Discovery (2013) (94)
Automated design of collective variables using supervised machine learning. (2018) (92)
Is the molten globule a third phase of proteins? (1998) (92)
Structural Insight into RNA Hairpin Folding Intermediates (2008) (91)
Nanotube confinement denatures protein helices. (2006) (88)
Beta-hairpin folding simulations in atomistic detail using an implicit solvent model. (2001) (87)
Does water play a structural role in the folding of small nucleic acids? (2005) (86)
Insights into nucleic acid conformational dynamics from massively parallel stochastic simulations. (2003) (86)
Parallelized-over-parts computation of absolute binding free energy with docking and molecular dynamics. (2006) (86)
Automated Discovery and Refinement of Reactive Molecular Dynamics Pathways. (2016) (85)
Transferable Neural Networks for Enhanced Sampling of Protein Dynamics. (2018) (83)
Unfolded-state dynamics and structure of protein L characterized by simulation and experiment. (2010) (83)
Calculations of the electric fields in liquid solutions. (2013) (80)
Critical assessment of nucleic acid electrostatics via experimental and computational investigation of an unfolded state ensemble. (2008) (80)
Persistent voids: a new structural metric for membrane fusion (2007) (79)
Marked difference in saxitoxin and tetrodotoxin affinity for the human nociceptive voltage-gated sodium channel (Nav1.7) (2012) (78)
Identification of significantly mutated regions across cancer types highlights a rich landscape of functional molecular alterations (2015) (78)
Side-chain recognition and gating in the ribosome exit tunnel (2008) (77)
Simulation of biomimetic recognition between polymers and surfaces. (1999) (77)
The predicted structure of the headpiece of the Huntingtin protein and its implications on Huntingtin aggregation. (2009) (77)
Perspective: Markov models for long-timescale biomolecular dynamics. (2014) (76)
Calculation of local water densities in biological systems: a comparison of molecular dynamics simulations and the 3D-RISM-KH molecular theory of solvation. (2011) (74)
Choosing weights for simulated tempering. (2007) (74)
Assessment of the protein‐structure refinement category in CASP8 (2009) (74)
Cooperativity, smooth energy landscapes and the origins of topology-dependent protein folding rates. (2003) (72)
Identification of simple reaction coordinates from complex dynamics. (2016) (72)
Advanced Potential Energy Surfaces for Molecular Simulation. (2016) (70)
Quantitative comparison of villin headpiece subdomain simulations and triplet–triplet energy transfer experiments (2011) (68)
Improvement in ADMET Prediction with Multitask Deep Featurization. (2020) (68)
Thermodynamic procedure to synthesize heteropolymers that can renature to recognize a given target molecule. (1994) (68)
Discovery of a regioselectivity switch in nitrating P450s guided by MD simulations and Markov models (2016) (68)
A new set of molecular mechanics parameters for hydroxyproline and its use in molecular dynamics simulations of collagen‐like peptides (2005) (67)
Perspective: Computational chemistry software and its advancement as illustrated through three grand challenge cases for molecular science. (2018) (66)
The Simbios National Center: Systems Biology in Motion (2008) (66)
Free energy landscape of activation in a signaling protein at atomic resolution (2015) (66)
Bayesian detection of intensity changes in single molecule and molecular dynamics trajectories. (2010) (65)
Transition path theory analysis of c-Src kinase activation (2016) (62)
Undermethylation associated with retroelement activation and chromosome remodelling in an interspecific mammalian hybrid (61)
One-dimensional reaction coordinate and the corresponding potential of mean force from commitment probability distribution. (2005) (60)
Chemical denaturants inhibit the onset of dewetting. (2008) (60)
CCMA: A Robust, Parallelizable Constraint Method for Molecular Simulations. (2010) (59)
Do conformational biases of simple helical junctions influence RNA folding stability and specificity? (2009) (59)
Bayesian comparison of Markov models of molecular dynamics with detailed balance constraint. (2009) (58)
Constructing Multi-Resolution Markov State Models (MSMs) to Elucidate RNA Hairpin Folding Mechanisms (2010) (58)
Convergence of folding free energy landscapes via application of enhanced sampling methods in a distributed computing environment. (2008) (57)
Dynamical reweighting: improved estimates of dynamical properties from simulations at multiple temperatures. (2011) (57)
Enumerations of the Hamiltonian walks on a cubic sublattice (1994) (56)
How Large is an α-Helix? Studies of the Radii of Gyration of Helical Peptides by Small-angle X-ray Scattering and Molecular Dynamics (2005) (55)
How accurate must potentials be for successful modeling of protein folding (1995) (55)
Precursor directed biosynthesis of an orthogonally functional erythromycin analogue: selectivity in the ribosome macrolide binding pocket. (2012) (55)
Validation of Markov state models using Shannon's entropy. (2006) (54)
Optimized parameter selection reveals trends in Markov state models for protein folding. (2016) (53)
Modeling Industrial ADMET Data with Multitask Networks (2016) (52)
Dynamic lattice Monte Carlo simulation of a model protein at an oil/water interface (2000) (52)
Molecular simulation of multistate peptide dynamics: A comparison between microsecond timescale sampling and multiple shorter trajectories (2008) (52)
The Fip35 WW domain folds with structural and mechanistic heterogeneity in molecular dynamics simulations. (2009) (52)
Mechanical Unfolding of a β-Hairpin Using Molecular Dynamics (2000) (52)
Network models for molecular kinetics and their initial applications to human health (2010) (51)
Characterization and rapid sampling of protein folding Markov state model topologies. (2011) (51)
Copernicus: A new paradigm for parallel adaptive molecular dynamics (2011) (50)
Polarizable atomic multipole X-ray refinement: application to peptide crystals (2009) (49)
A molecular interpretation of 2D IR protein folding experiments with Markov state models. (2014) (48)
Bayesian energy landscape tilting: towards concordant models of molecular ensembles. (2014) (48)
Conformational heterogeneity of the calmodulin binding interface (2016) (48)
Polymer gels that can recognize and recover molecules (1995) (48)
Optimal use of data in parallel tempering simulations for the construction of discrete-state Markov models of biomolecular dynamics. (2011) (48)
Emergence of glass-like behavior in Markov state models of protein folding dynamics. (2013) (47)
Empirical force‐field assessment: The interplay between backbone torsions and noncovalent term scaling (2005) (47)
Towards simple kinetic models of functional dynamics for a kinase subfamily (2017) (47)
Cloud computing approaches for prediction of ligand binding poses and pathways (2015) (46)
A Role for Confined Water in Chaperonin Function (2008) (46)
Effects of familial mutations on the monomer structure of Aβ₄₂. (2012) (46)
Foldamer dynamics expressed via Markov state models. I. Explicit solvent molecular-dynamics simulations in acetonitrile, chloroform, methanol, and water. (2005) (46)
Folding thermodynamics and kinetics of imprinted renaturable heteropolymers (1994) (45)
Weakly-Supervised Deep Learning of Heat Transport via Physics Informed Loss (2018) (45)
N-Body simulation on GPUs (2006) (44)
Does native state topology determine the RNA folding mechanism? (2004) (44)
Millisecond dynamics of BTK reveal kinome-wide conformational plasticity within the apo kinase domain (2017) (43)
Splitting probabilities as a test of reaction coordinate choice in single-molecule experiments. (2011) (42)
Design of β-amyloid aggregation inhibitors from a predicted structural motif. (2012) (42)
Learning Kinetic Distance Metrics for Markov State Models of Protein Conformational Dynamics. (2013) (42)
A network of molecular switches controls the activation of the two-component response regulator NtrC (2015) (41)
Accelerated Molecular Dynamics Simulations with the AMOEBA Polarizable Force Field on Graphics Processing Units (2013) (41)
Structural correspondence between the α-helix and the random-flight chain resolves how unfolded proteins can have native-like properties (2003) (41)
Water ordering at membrane interfaces controls fusion dynamics. (2011) (41)
Complex pathways in folding of protein G explored by simulation and experiment. (2014) (41)
Pre-training Graph Neural Networks (2019) (40)
Non-Bulk-Like Solvent Behavior in the Ribosome Exit Tunnel (2010) (39)
N-Body Simulations on GPUs (2007) (38)
Dimerization of the p53 oligomerization domain: identification of a folding nucleus by molecular dynamics simulations. (2005) (38)
K-Means for Parallel Architectures Using All-Prefix-Sum Sorting and Updating Steps (2013) (37)
Multiscale Dynamics of Macromolecules Using Normal Mode Langevin (2010) (37)
Engineering a Single-Agent Cytokine/Antibody Fusion That Selectively Expands Regulatory T Cells for Autoimmune Disease Therapy (2018) (37)
Osprey: Hyperparameter Optimization for Machine Learning (2016) (36)
On the theory of folding kinetics for short proteins. (1997) (36)
Kinetic definition of protein folding transition state ensembles and reaction coordinates. (2006) (35)
Ward Clustering Improves Cross-Validated Markov State Models of Protein Folding. (2017) (35)
United polarizable multipole water model for molecular mechanics simulation. (2015) (35)
Polarizable Atomic Multipole X-Ray Refinement: Particle Mesh Ewald Electrostatics for Macromolecular Crystals. (2011) (34)
Simulating oligomerization at experimental concentrations and long timescales: A Markov state model approach. (2008) (34)
Increased detection of structural templates using alignments of designed sequences (2003) (34)
The solvation interface is a determining factor in peptide conformational preferences. (2006) (34)
A-Site Residues Move Independently from P-Site Residues in all-Atom Molecular Dynamics Simulations of the 70S Bacterial Ribosome (2012) (33)
PAPER—Accelerating parallel evaluations of ROCS (2010) (33)
Normal mode partitioning of Langevin dynamics for biomolecules. (2008) (32)
Bayesian single-exponential kinetics in single-molecule experiments and simulations. (2009) (32)
Anatomy of High-Performance 2D Similarity Calculations (2011) (32)
Combining molecular dynamics with bayesian analysis to predict and evaluate ligand-binding mutations in influenza hemagglutinin. (2009) (31)
Simulated tempering yields insight into the low‐resolution Rosetta scoring functions (2009) (31)
Reintroducing electrostatics into macromolecular crystallographic refinement: application to neutron crystallography and DNA hydration. (2011) (31)
On the role of conformational geometry in protein folding (1999) (31)
Markov State Models and tICA Reveal a Nonnative Folding Nucleus in Simulations of NuG2. (2016) (31)
Storage@home: Petascale Distributed Storage (2007) (30)
CAMPAIGN: an open-source library of GPU-accelerated data clustering algorithms (2011) (30)
Phase Diagram of Heteropolymers with an Imprinted Conformation (1995) (30)
Accelerating molecular dynamic simulation on the cell processor and Playstation 3 (2009) (30)
Foldamer dynamics expressed via Markov state models. II. State space decomposition. (2005) (30)
Solvent viscosity dependence of the protein folding dynamics. (2008) (29)
Observation of correlated X-ray scattering at atomic resolution (2014) (29)
Folding and misfolding of the collagen triple helix: Markov analysis of molecular dynamics simulations. (2007) (28)
Local structure formation in simulations of two small proteins. (2007) (28)
Potential for modulation of the hydrophobic effect inside chaperonins. (2008) (27)
Quercitrin and quercetin 3-&bgr;-D-glucoside as chemical chaperones for the A4V SOD1 ALS-causing mutant (2017) (27)
REDOR NMR Reveals Multiple Conformers for a Protein Kinase C Ligand in a Membrane Environment (2018) (27)
Efficient maximum likelihood parameterization of continuous-time Markov processes. (2015) (26)
Thermodynamics of the coil to frozen globule transition in heteropolymers (1997) (26)
Simple theory of protein folding kinetics. (2010) (26)
Persistent Topology and Metastable State in Conformational Dynamics (2013) (26)
Using Deep Learning for Segmentation and Counting within Microscopy Data (2018) (26)
Polarizable atomic multipole x-ray refinement: hydration geometry and application to macromolecules. (2010) (26)
Solving the RNA design problem with reinforcement learning (2018) (26)
SIML: A Fast SIMD Algorithm for Calculating LINGO Chemical Similarities on GPUs and CPUs (2010) (26)
Structural basis for influence of viral glycans on ligand binding by influenza hemagglutinin. (2008) (26)
Deep Neural Network Computes Electron Densities and Energies of a Large Set of Organic Molecules Faster than Density Functional Theory (DFT) (2018) (26)
Dynamical phase transitions reveal amyloid-like states on protein folding landscapes. (2014) (25)
How does averaging affect protein structure comparison on the ensemble level? (2004) (25)
Modeling the mechanism of CLN025 beta-hairpin formation. (2017) (25)
Theory for an order-driven disruption of the liquid state in water. (2008) (24)
Comparison of computational approaches for predicting the effects of missense mutations on p53 function. (2009) (24)
Simulated unfolded-state ensemble and the experimental NMR structures of villin headpiece yield similar wide-angle solution X-ray scattering profiles. (2006) (24)
ELECTRON TRANSPORT IN DISORDERED POLYMERIC AND BIOLOGICAL SYSTEMS (1997) (24)
Rattling the cage: computational models of chaperonin-mediated protein folding. (2008) (24)
Foldamer simulations: novel computational methods and applications to poly-phenylacetylene oligomers. (2004) (24)
Meeting halfway on the bridge between protein folding theory and experiment (2003) (23)
Introduction and overview of this book. (2014) (23)
Molecular dynamics simulation of lipid reorientation at bilayer edges. (2004) (23)
Computationally Discovered Potentiating Role of Glycans on NMDA Receptors (2016) (23)
Effects of long‐range electrostatic forces on simulated protein folding kinetics (2008) (22)
A modular DNA scaffold to study protein–protein interactions at single-molecule resolution (2019) (22)
MSMExplorer: visualizing Markov state models for biomolecule folding simulations (2013) (21)
On the role of chemical detail in simulating protein folding kinetics (2006) (21)
Statistical model selection for Markov models of biomolecular dynamics. (2014) (21)
Heat dissipation guides activation in signaling proteins (2015) (21)
Mechanical unfolding of a beta-hairpin using molecular dynamics. (2000) (20)
Tungstate as a Transition State Analog for Catalysis by Alkaline Phosphatase. (2016) (20)
Sequence Coevolution between RNA and Protein Characterized by Mutual Information between Residue Triplets (2012) (19)
Note: MSM lag time cannot be used for variational model selection. (2017) (19)
Folding probabilities: a novel approach to folding transitions and the two-dimensional Ising-model. (2004) (19)
Long Timestep Molecular Dynamics on the Graphical Processing Unit. (2013) (19)
Automatic Selection of Order Parameters in the Analysis of Large Scale Molecular Dynamics Simulations (2014) (19)
A smoothly decoupled particle interface: new methods for coupling explicit and implicit solvent. (2011) (19)
Building Markov state models with solvent dynamics (2013) (19)
Understanding Protein Dynamics with L1-Regularized Reversible Hidden Markov Models (2014) (18)
Kinetic computational alanine scanning: application to p53 oligomerization. (2006) (18)
How to create polymers with protein-like capabilities: a theoretical suggestion (1997) (18)
Solution-Phase Conformation and Dynamics of Conjugated Isoindigo-Based Donor-Acceptor Polymer Single Chains. (2017) (18)
A Minimum Variance Clustering Approach Produces Robust and Interpretable Coarse-Grained Models. (2017) (17)
Molecular Dynamics Study of the Structure Organization in Strongly Coupled Chain of Charged Particles (1997) (17)
Landmark Kernel tICA for Conformational Dynamics (2017) (17)
A New Twist on the Helix-Coil Transition: A Non-Biological Helix with Protein-Like Intermediates and Traps (2001) (17)
Bayesian update method for adaptive weighted sampling. (2006) (17)
Reducing the effect of Metropolization on mixing times in molecular dynamics simulations. (2012) (16)
Step Change Improvement in ADMET Prediction with PotentialNet Deep Featurization (2019) (16)
Chemical Kinetics and Mechanisms of Complex Systems: A Perspective on Recent Theoretical Advances (2014) (16)
Classical Quantum Optimization with Neural Network Quantum States. (2019) (16)
Rationally Designed Turn Promoting Mutation in the Amyloid-β Peptide Sequence Stabilizes Oligomers in Solution (2011) (16)
Applications of free energy calculations to chemistry and biology (2007) (16)
ROCS-derived features for virtual screening (2016) (16)
Inferring the Rate-Length Law of Protein Folding (2013) (15)
Bayesian analysis of isothermal titration calorimetry for binding thermodynamics (2018) (15)
Simulated Dynamics of Glycans on Ligand-Binding Domain of NMDA Receptors Reveals Strong Dynamic Coupling between Glycans and Protein Core. (2017) (15)
Corrigendum to “Simulation of Folding of a Small Alpha-helical Protein in Atomistic Detail using Worldwide-distributed Computing” (2002) (15)
Phase diagram of imprinted copolymers (1994) (14)
Transfer Learning from Markov Models Leads to Efficient Sampling of Related Systems. (2017) (14)
Probing the origins of two-state folding. (2013) (14)
A simple model predicts experimental folding rates and a hub-like topology. (2012) (14)
Discovery of novel brain permeable and G protein-biased beta-1 adrenergic receptor partial agonists for the treatment of neurocognitive disorders (2017) (14)
Protein folding is mechanistically robust. (2012) (14)
Calculation of rate spectra from noisy time series data (2012) (14)
A universal TANGO? (2004) (13)
MSMExplorer: Data Visualizations for Biomolecular Dynamics (2017) (13)
SentRNA: Improving computational RNA design by incorporating a prior of human design strategies (2018) (13)
Training and Validation of a Liquid-Crystalline Phospholipid Bilayer Force Field. (2016) (13)
Finite domain simulations with adaptive boundaries: accurate potentials and nonequilibrium movesets. (2013) (13)
Statistical Characterization of Protein Ensembles (2008) (13)
The social network (of protein conformations) (2011) (12)
Molecular dynamics simulations for the ranking, evaluation, and refinement of computationally designed proteins. (2013) (12)
SCISSORS: A Linear-Algebraical Technique to Rapidly Approximate Chemical Similarities (2010) (12)
Sequence optimization for native state stability determines the evolution and folding kinetics of a small protein. (2003) (12)
Conserve Water: A Method for the Analysis of Solvent in Molecular Dynamics. (2015) (12)
Inside the chaperonin toolbox: theoretical and computational models for chaperonin mechanism (2009) (12)
Understanding protein folding using Markov state models. (2014) (12)
Charge, hydrophobicity, and confined water: putting past simulations into a simple theoretical framework. (2010) (12)
How large is an alpha-helix? Studies of the radii of gyration of helical peptides by small-angle X-ray scattering and molecular dynamics. (2005) (12)
Computational IR Spectroscopy of Insulin Dimer Structure and Conformational Heterogeneity. (2021) (11)
Freezing of compact random heteropolymers with correlated sequence fluctuations (1998) (11)
Spatial Graph Convolutions for Drug Discovery (2018) (11)
Atomistic structural ensemble refinement reveals non-native structure stabilizes a sub-millisecond folding intermediate of CheY (2017) (11)
An information theoretic framework reveals a tunable allosteric network in group II chaperonins (2017) (11)
Markov modeling reveals novel intracellular modulation of the human TREK-2 selectivity filter (2016) (11)
Intradomain Interactions in an NMDA Receptor Fragment Mediate N-Glycan Processing and Conformational Sampling. (2019) (10)
Phase diagram of an imprinted copolymer in a random external field (1995) (10)
Communication: Adaptive boundaries in multiscale simulations. (2018) (10)
MDEntropy: Information-Theoretic Analyses for Molecular Dynamics (2017) (9)
Computer Simulations Predict High Structural Heterogeneity of Functional State of NMDA Receptors (2017) (9)
The Roles of Entropy and Kinetics in Structure Prediction (2009) (9)
Atomistic protein folding simulations on the hundreds of microsecond timescale using worldwide distributed computing (2002) (9)
Elucidating Ligand-Modulated Conformational Landscape of GPCRs Using Cloud-Computing Approaches. (2015) (9)
Length dependent folding kinetics of phenylacetylene oligomers: structural characterization of a kinetic trap. (2005) (9)
Improved Training with Curriculum GANs (2018) (9)
Simbios: an NIH national center for physics-based simulation of biological structures (2012) (9)
A robust approach to estimating rates from time-correlation functions (2011) (9)
The Dynamic Conformational Cycle of the Group I Chaperonin C-Termini Revealed via Molecular Dynamics Simulation (2015) (9)
Kinetic Machine Learning Unravels Ligand-Directed Conformational Change of μ Opioid Receptor (2017) (9)
Binding Pathway of Opiates to μ-Opioid Receptors Revealed by Machine Learning (2018) (8)
Physical machine learning outperforms "human learning" in Quantum Chemistry (2019) (8)
Markov State Models of Millisecond Folder ACBP Reveals New Views of the Folding Reaction (2011) (8)
Probing the Nanosecond Dynamics of a Designed Three-Stranded Beta-Sheet with a Massively Parallel Molecular Dynamics Simulation (2009) (8)
Machine Learning Harnesses Molecular Dynamics to Discover New $\mu$ Opioid Chemotypes (2018) (8)
Efficient gaussian density formulation of volume and surface areas of macromolecules on graphical processing units (2017) (7)
Corrigendum: Discovering chemistry with an ab initio nanoreactor (2015) (6)
Predicting Structure and Dynamics of Loosely-Ordered Protein Complexes: Influenza Hemagglutinin Fusion Peptide (2006) (6)
Deep Learning Phase Segregation (2018) (6)
Dynamical model of the CLC-2 ion channel reveals conformational changes associated with selectivity-filter gating (2019) (6)
A Fast 3 × N Matrix Multiply Routine for Calculation of Protein RMSD (2014) (5)
Note: Variational Encoding of Protein Dynamics Benefits from Maximizing Latent Autocorrelation (2018) (5)
A bundling of viral fusion mechanisms (2011) (5)
Cross-Graining: Efficient Multi-Scale Simulation via Markov State Models (2010) (5)
Bayesian regularization of the length of memory in reversible sequences (2016) (5)
Functional understanding of solvent structure in GroEL cavity through dipole field analysis. (2013) (5)
Percolation-like phase transitions in network models of protein dynamics. (2015) (5)
Erratum: Splitting Probabilities as a Test of Reaction Coordinate Choice in Single-Molecule Experiments [Phys. Rev. Lett. 107, 098102 (2011)] (2012) (5)
Modelling Intrinsically Disordered Protein Dynamics as Networks of Transient Secondary Structure (2018) (5)
Accelerating Development and Execution Speed with Just-in-Time GPU Code Generation (2012) (5)
Dimerization of the p 53 Oligomerization Domain : Identification of a Folding Nucleus by Molecular Dynamics Simulations Lillian (2004) (5)
Combining Mutual Information with Structural Analysis to Screen for Functionally Important Residues in Influenza Hemagglutinin (2008) (5)
Unsupervised learning of dynamical and molecular similarity using variance minimization (2017) (4)
Forcebalance: a Systematic, Reproducible, Statistically Driven Approach to More Accurate Molecular Dynamics Models (2014) (4)
Efficient inference of protein structural ensembles (2014) (4)
Error Bounds on the SCISSORS Approximation Method (2011) (4)
Bayesian inference for Brownian dynamics. (2010) (4)
Energy Conservation as a Measure of Simulation Accuracy (2016) (4)
Entropy-production-driven oscillators in simple nonequilibrium networks. (2015) (4)
Folding pathway of a lattice model for protein folding (1998) (3)
Decision functions from supervised machine learning algorithms as collective variables for accelerating molecular simulations (2018) (3)
Systematic identification of significantly mutated regions reveals a rich landscape of functional molecular alterations across cancer genomes (2015) (3)
Synthesis of spiro-2,6-dioxopiperazine and spiro-2,6-dioxopyrazine scaffolds using amino acids in a three-component reaction to generate potential Sigma-1 (σ1) receptor selective ligands. (2019) (3)
Bayesian Energy Landscape Tilting: Towards Concordant Models of Molecular Ensembles (2014) (3)
Erratum: Random-coil behavior and the dimensions of chemically unfolded proteins (Proceedings of The National Academy of Sciences of The United States of America (August 24, 2004) 101, 34 (12491-12496)) (2005) (3)
SCISSORS: Practical Considerations (2014) (3)
Potential-based dynamical reweighting for Markov state models of protein dynamics. (2015) (3)
(Compressed) sensing and sensibility (2011) (3)
Large-Scale Chemical Informatics on GPUs (2011) (3)
A Targeted Computational Screen of the SWEETLEAD Database Reveals FDA-Approved Compounds with Anti-Dengue Viral Activity (2020) (3)
Theoretical restrictions on longest implicit time scales in Markov state models of biomolecular dynamics. (2017) (3)
Corrigendum: Conformational heterogeneity of the calmodulin binding interface (2016) (2)
Chapter 8:Computer Simulations of Protein Folding (2008) (2)
Adaptive Seeding: A New Method for Simulating Biologically Relevant Timescales (2009) (2)
folding stability and specificity ? Do conformational biases of simple helical junctions influence RNA Material Supplemental (2009) (2)
Dynamical model of the CLC-2 ion channel exhibits a two-step gating mechanism (2017) (2)
Eigenvalues of the homogeneous finite linear one step master equation: applications to downhill folding. (2012) (2)
Application of new informatics tools for identifying allosteric lead ligands of the c-Src kinase (2016) (2)
Activation Mechanism of a Signaling Protein at Atomic Resolution (2015) (2)
Corrigendum: Cloud-based simulations on Google Exacycle reveal ligand modulation of GPCR activation pathways. (2015) (2)
Modeling the Mechanism of CLN025 Beta-Hairpin Formation (2017) (2)
Inclusion of persistence length-based secondary structure in replica field theoretic models of heteropolymer freezing. (2013) (2)
Derivation and assessment of phase-shifted, disordered vector field models for frustrated solvent interactions. (2013) (2)
A Fast Geometric Clustering Method on Conformation Space of Biomolecules (2009) (1)
A Multiscale Approach to Sampling Nascent Peptide Chains in the Ribosomal Exit Tunnel (2008) (1)
Deep Learning Fluid Mechanics (2017) (1)
Erratum: “Comparison of efficiency and bias of free energies computed by exponential averaging, the Bennett acceptance ratio, and thermodynamic integration” [J. Chem. Phys. 122, 144107 (2005)] (2008) (1)
Addendum to “Heterogeneity Even at the Speed Limit of Folding: Large-Scale Molecular Dynamics Study of a Fast-Folding Variant of the Villin Headpiece” [J. Mol. Biol. 374 (2007) 806–816] (2008) (1)
Freezing transition of heteropolymers (1995) (1)
of structural ensembles Thoroughly sampling sequence space : Large-scale protein design (2002) (1)
Physical Chemistry Principles (2012) (1)
Building Markov state models with solvent dynamics (2013) (1)
Adaptive boundaries in multiscale simulations (2018) (1)
Learning Protein Dynamics with Metastable Switching Systems (2016) (1)
Predicting Toxicity from Gene Expression with Neural Networks (2019) (1)
Computational Nanomedicine: Simulating Protein Misfolding Disease (2010) (1)
Chaperonins: The Machines Which Fold Proteins (2011) (1)
2D compact model to characterize phase separation in organic solar cell bulk heterojunctions (Conference Presentation) (2017) (0)
Bayesian Modeling of Crystallographic Disorder (2012) (0)
Understanding how Beta-Hairpins Fold using Molecular Dynamics Simulations in Multiple Force Fields (2018) (0)
of Core Topology and Composition on the Structure and Kinetics of Star Polymers: A Molecular Dynamics Study. (2018) (0)
Adaptive Boundaries in Multi-Resolution Simulations (2015) (0)
Shared Memory and Hardware Utilizations for the Parallelization of Local Sequences Alignment using SW Algorithm: A Review (2016) (0)
Probing the Relationship between Extracellular Ligand Recognition and Cytokine Receptor Activation with Structural Biology and Protein Engineering (2013) (0)
Millisecond Timescale, Atomistic Protein Folding Simulations Yield a Network Theory for Protein Folding (2010) (0)
Accelerating the Molecular Dynamics Sampling of Mutants: A Hierarchical Bayesian Markov State Model Strategy (2014) (0)
Simulating protein folding and aggregation on the 10 second timescale (2007) (0)
Millisecond dynamics of BTK reveal kinome-wide conformational plasticity within the apo kinase domain (2017) (0)
Inferring Structural Ensembles from Noisy Experiments and Molecular Dynamics: Correcting Force Field Bias with Bayesian Energy Landscape Tilting (2014) (0)
A Modular DNA Scaffold to Study Protein-Protein Interactions at Single-Molecule Resolution (2020) (0)
Statistical Characterization of Protein Ensembles (PREPRINT) (2006) (0)
Hierarchical Clustering of Markov State Models Reveals Sequence Effects in p53-CTD Dynamic Behavior (2018) (0)
X-Ray Crystallography Refinement as Ewald Intended: From Drug Design to Ribosome Crystals (2010) (0)
Simulating protein folding with full atomistic detail (2007) (0)
Diffusion of Unfolded Acyl-Coenzyme A-Binding Protein Over a Complete Range of Denaturant (2011) (0)
From Aminomutases to Ammonia Lyases (2014) (0)
Folding@home: achievements from over twenty years of citizen science herald the exascale era. (2023) (0)
MDTraj 1.4.2 (2015) (0)
Reintroducing Electrostatics into Macromolecular Crystallographic Refinement: Z-DNA (X-ray) (2011) (0)
Markov modeling reveals novel intracellular modulation of the human TREK-2 selectivity filter (2017) (0)
Statistical Learning and Docking Recover the Reaction Coordinates of a GPCR (2016) (0)
Investigating Ligand-Modulation of GPCR Activation Pathways (2014) (0)
Protein Folding: Detailed Models (2005) (0)
Calculations of the Electric Field in Solutions and Proteins with Polarizable Force Fields (2014) (0)
IL-2 mutant D10 ternary complex (2012) (0)
A Simple Model of Protein Folding Thermodynamics and Kinetics (1997) (0)
Transfer Learning from Markov models leads to efficient sampling of related systems (2017) (0)
Atomic-Resolution Simulations Yield New Insight into Vesicle Fusion and Fusion Protein Mechanisms (2010) (0)
Title Finding Our Way in the Dark Proteome Permalink (2016) (0)
Toward a Global View of the Conformational Landscape of the Human Kinome (2014) (0)
A Well-controlled Fast Clustering Method on Conformation Space of Biomolecules (2008) (0)
Crystal Structure of the Group II Chaperonin from Methanococcus Maripaludis, Cysteine-less mutant in the Apo State (2018) (0)
Thalweg: A framework for programming 1,000 machines with 1,000 cores (2009) (0)
Transferable tICA-Metadynamics: Efficient sampling of protein mutants by transferring information from the wild type's Markov state model (2017) (0)
Computer Simulations of Protein Folding (2008) (0)
Computational Evaluation of Mutational Effects on Kinase Dynamics (2016) (0)
CFTR misfolds during native-centric simulations due to entropic penalties of native state formation (2018) (0)
Constructing a Flexible Internet-Scale Time-Sharing System using Deterministic Checkpointing (2010) (0)
3-D Particle Simulation of Strongly-Coupled Chains of Charged Polymers (1996) (0)
Dynamic Feature Extraction from Molecular Mechanics Trajectories (2013) (0)
Analysis Of Influenza Hemagglutinin Ligand-binding From Mutational Data And Molecular Motion (2009) (0)
Molecular dynamics simulations reveal ligand-controlled positioning of a peripheral protein complex in membranes (2017) (0)
Activation Pathways of Kinases Reveal Intermediate States as Novel Targets for Drug Design (2014) (0)
Correction (2012) (0)
Crystal Structure of the Group II Chaperonin from Methanococcus Maripaludis D386ADeltaLid Mutant in the Open, ADP-Bound State (2018) (0)
Activation Dynamics of Sodium Ion Channel (2016) (0)
Revealing the Early Events of ACBP Folding by Ultrarapid Mixing (2011) (0)
Predicting Gene Expression Between Species with Neural Networks (2019) (0)
Computational simulation of lipid bilayer reorientation at gaps (2003) (0)
Landau-type expansion for the energy landscape of the designed heteropolymer (1997) (0)
Folding@home: achievements from over twenty years of citizen science herald the exascale era (2023) (0)
Freezing of Random and Designed Heteropolymers: Replica Solution Without Replicas (1996) (0)
Understanding Protein Folding Yields Important Insights into Protein Conformational Change: New Insights into Kinases and GPCRs (2015) (0)
REP-X: An Evolution-guided Strategy for the Rational Design of Cysteine-less Protein Variants (2020) (0)
REP-X: An Evolution-guided Strategy for the Rational Design of Cysteine-less Protein Variants (2019) (0)
Deep Learning Physical Phenomena (2018) (0)
Title Accelerated molecular dynamics simulations with the AMOEBA polarizable force field on graphics processing units Permalink (2013) (0)
Lessons from 8 Milliseconds of Aggregated Kinase Molecular Dynamics Simulations (2018) (0)
Glycan-Protein Interactions in NMDA Receptors Revealed with Computational Modeling and NMR Spectroscopy (2018) (0)
Connecting Unfolded Protein Dynamics and Aggregation (2010) (0)
Directed evolution and rational design of a de novo designed esterase toward improved catalysis. Northeast Structural Genomics Consortium (NESG) Target OR184 (2013) (0)
Breaking protein-protein interactions: A combined chemical and computational approach to develop a new class of protein aggregation inhibitors (2009) (0)
On the Origins of Regulated Disorder within the C-Terminus of P53 (2018) (0)
Large-Scale ChemicalInformatics on GPUs (2011) (0)
Interleukin-2 mutant D10 (2012) (0)
Is Theory Leading Neutron Diffraction in Macromolecular Solvent Networks (2010) (0)

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