Vijay S. Pande

According to our database1, Vijay S. Pande authored at least 67 papers between 2003 and 2020.

Collaborative distances:



In proceedings 
PhD thesis 




Dynamical model of the CLC-2 ion channel reveals conformational changes associated with selectivity-filter gating.
PLoS Comput. Biol., 2020

Strategies for Pre-training Graph Neural Networks.
Proceedings of the 8th International Conference on Learning Representations, 2020

Pre-training Graph Neural Networks.
CoRR, 2019

Step Change Improvement in ADMET Prediction with PotentialNet Deep Featurization.
CoRR, 2019

Solving the RNA design problem with reinforcement learning.
PLoS Comput. Biol., 2018

Weakly-Supervised Deep Learning of Heat Transport via Physics Informed Loss.
CoRR, 2018

Improved Training with Curriculum GANs.
CoRR, 2018

Deep Learning Phase Segregation.
CoRR, 2018

Note: Variational Encoding of Protein Dynamics Benefits from Maximizing Latent Autocorrelation.
CoRR, 2018

Spatial Graph Convolutions for Drug Discovery.
CoRR, 2018

SentRNA: Improving computational RNA design by incorporating a prior of human design strategies.
CoRR, 2018

Using Deep Learning for Segmentation and Counting within Microscopy Data.
CoRR, 2018

Decision functions from supervised machine learning algorithms as collective variables for accelerating molecular simulations.
CoRR, 2018

Graph Convolutional Policy Network for Goal-Directed Molecular Graph Generation.
Proceedings of the Advances in Neural Information Processing Systems 31: Annual Conference on Neural Information Processing Systems 2018, 2018

OpenMM 7: Rapid development of high performance algorithms for molecular dynamics.
PLoS Comput. Biol., 2017

MDEntropy: Information-Theoretic Analyses for Molecular Dynamics.
J. Open Source Softw., 2017

MSMExplorer: Data Visualizations for Biomolecular Dynamics.
J. Open Source Softw., 2017

Efficient gaussian density formulation of volume and surface areas of macromolecules on graphical processing units.
J. Comput. Chem., 2017

Deep Learning the Physics of Transport Phenomena.
CoRR, 2017

MoleculeNet: A Benchmark for Molecular Machine Learning.
CoRR, 2017

Retrosynthetic reaction prediction using neural sequence-to-sequence models.
CoRR, 2017

Atomic Convolutional Networks for Predicting Protein-Ligand Binding Affinity.
CoRR, 2017

Osprey: Hyperparameter Optimization for Machine Learning.
J. Open Source Softw., 2016

Computational Modeling of β-Secretase 1 (BACE-1) Inhibitors Using Ligand Based Approaches.
J. Chem. Inf. Model., 2016

ROCS-derived features for virtual screening.
J. Comput. Aided Mol. Des., 2016

Molecular graph convolutions: moving beyond fingerprints.
J. Comput. Aided Mol. Des., 2016

Learning Protein Dynamics with Metastable Switching Systems.
CoRR, 2016

Low Data Drug Discovery with One-shot Learning.
CoRR, 2016

Massively Multitask Networks for Drug Discovery.
CoRR, 2015

SCISSORS: Practical Considerations.
J. Chem. Inf. Model., 2014

Understanding Protein Dynamics with L1-Regularized Reversible Hidden Markov Models.
Proceedings of the 31th International Conference on Machine Learning, 2014

K-Means for Parallel Architectures Using All-Prefix-Sum Sorting and Updating Steps.
IEEE Trans. Parallel Distributed Syst., 2013

Building Markov state models with solvent dynamics.
BMC Bioinform., 2013

Simbios: an NIH national center for physics-based simulation of biological structures.
J. Am. Medical Informatics Assoc., 2012

Anatomy of High-Performance 2D Similarity Calculations.
J. Chem. Inf. Model., 2011

Error Bounds on the SCISSORS Approximation Method.
J. Chem. Inf. Model., 2011

CAMPAIGN: an open-source library of GPU-accelerated data clustering algorithms.
Bioinform., 2011

Copernicus: a new paradigm for parallel adaptive molecular dynamics.
Proceedings of the Conference on High Performance Computing Networking, 2011

Non-Bulk-Like Solvent Behavior in the Ribosome Exit Tunnel.
PLoS Comput. Biol., 2010

Atomic-Resolution Simulations Predict a Transition State for Vesicle Fusion Defined by Contact of a Few Lipid Tails.
PLoS Comput. Biol., 2010

SIML: A Fast SIMD Algorithm for Calculating LINGO Chemical Similarities on GPUs and CPUs.
J. Chem. Inf. Model., 2010

SCISSORS: A Linear-Algebraical Technique to Rapidly Approximate Chemical Similarities.
J. Chem. Inf. Model., 2010

PAPER - Accelerating parallel evaluations of ROCS.
J. Comput. Chem., 2010

Efficient nonbonded interactions for molecular dynamics on a graphics processing unit.
J. Comput. Chem., 2010

OpenMM: A Hardware-Independent Framework for Molecular Simulations.
Comput. Sci. Eng., 2010

Cross-Graining: Efficient Multi-Scale Simulation via Markov State Models.
Proceedings of the Biocomputing 2010: Proceedings of the Pacific Symposium, 2010

Multiscale Dynamics of Macromolecules Using Normal Mode Langevin.
Proceedings of the Biocomputing 2010: Proceedings of the Pacific Symposium, 2010

Constructing Multi-Resolution Markov State Models (MSMs) to Elucidate RNA Hairpin Folding Mechanisms.
Proceedings of the Biocomputing 2010: Proceedings of the Pacific Symposium, 2010

Hard Data on Soft Errors: A Large-Scale Assessment of Real-World Error Rates in GPGPU.
Proceedings of the 10th IEEE/ACM International Conference on Cluster, 2010

Accelerating molecular dynamic simulation on the cell processor and Playstation 3.
J. Comput. Chem., 2009

Accelerating molecular dynamic simulation on graphics processing units.
J. Comput. Chem., 2009

A Multiscale Approach to Sampling Nascent Peptide Chains in the Ribosomal Exit Tunnel.
Proceedings of the Biocomputing 2009: Proceedings of the Pacific Symposium, 2009

Combining Mutual Information with Structural Analysis to Screen for Functionally Important Residues in Influenza Hemagglutinin.
Proceedings of the Biocomputing 2009: Proceedings of the Pacific Symposium, 2009

Thalweg: A framework for programming 1, 000 machines with 1, 000 cores.
Proceedings of the 23rd IEEE International Symposium on Parallel and Distributed Processing, 2009

Folding@home: Lessons from eight years of volunteer distributed computing.
Proceedings of the 23rd IEEE International Symposium on Parallel and Distributed Processing, 2009

The Simbios National Center: Systems Biology in Motion.
Proc. IEEE, 2008

Effects of long-range electrostatic forces on simulated protein folding kinetics.
J. Comput. Chem., 2008

Molecular simulation of multistate peptide dynamics: A comparison between microsecond timescale sampling and multiple shorter trajectories.
J. Comput. Chem., 2008

Control of Membrane Fusion Mechanism by Lipid Composition: Predictions from Ensemble Molecular Dynamics.
PLoS Comput. Biol., 2007

N-Body Simulations on GPUs
CoRR, 2007

Persistent voids: a new structural metric for membrane fusion.
Bioinform., 2007

Predicting Structure and Dynamics of Loosely-Ordered Protein Complexes: Influenza Hemagglutinin Fusion Peptide.
Proceedings of the Biocomputing 2007, 2007

Storage@home: Petascale Distributed Storage.
Proceedings of the 21th International Parallel and Distributed Processing Symposium (IPDPS 2007), 2007

Poster reception - N-Body simulation on GPUs.
Proceedings of the ACM/IEEE SC2006 Conference on High Performance Networking and Computing, 2006

Empirical force-field assessment: The interplay between backbone torsions and noncovalent term scaling.
J. Comput. Chem., 2005

A new set of molecular mechanics parameters for hydroxyproline and its use in molecular dynamics simulations of collagen-like peptides.
J. Comput. Chem., 2005

Computational Simulation of Lipid Bilayer Reorientation at Gaps.
Proceedings of the 2nd IEEE Computer Society Bioinformatics Conference, 2003