Vijay S. Pande
American scientist
Vijay S. Pande's AcademicInfluence.com Rankings
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Chemistry Engineering
Vijay S. Pande's Degrees
- Bachelors Chemical Engineering University of California, Berkeley
Why Is Vijay S. Pande Influential?
(Suggest an Edit or Addition)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.
Vijay S. Pande's Published Works
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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