Vijay S. Pande

Publication Activity (10 Years)

Years Active: 2003-2023
Publications (10 Years): 33

Top Topics

Machine Learning

Predicting Protein

Top Venues

J. Chem. Inf. Model.

PLoS Comput. Biol.

J. Open Source Softw.

Publications

Peter K. Eastman, Raimondas Galvelis, Raúl P. Peláez, Charlles R. A. Abreu, Stephen E. Farr, Emilio Gallicchio, Anton Gorenko, Michael M. Henry, Frank Hu, Jing Huang, Andreas Krämer, Julien Michel, Joshua A. Mitchell, Vijay S. Pande, João P. G. L. M. Rodrigues, Jaime Rodríguez-Guerra, Andrew C. Simmonett, Jason M. Swails, Ivy Zhang, John D. Chodera, Gianni De Fabritiis, Thomas E. Markland
OpenMM 8: Molecular Dynamics Simulation with Machine Learning Potentials. CoRR (2023)
Keri A. McKiernan, Anna K. Koster, Merritt Maduke, Vijay S. Pande
Dynamical model of the CLC-2 ion channel reveals conformational changes associated with selectivity-filter gating. PLoS Comput. Biol. 16 (3) (2020)
Weihua Hu, Bowen Liu, Joseph Gomes, Marinka Zitnik, Percy Liang, Vijay S. Pande, Jure Leskovec
Strategies for Pre-training Graph Neural Networks. ICLR (2020)
Weihua Hu, Bowen Liu, Joseph Gomes, Marinka Zitnik, Percy Liang, Vijay S. Pande, Jure Leskovec
Pre-training Graph Neural Networks. CoRR (2019)
Evan N. Feinberg, Robert P. Sheridan, Elizabeth Joshi, Vijay S. Pande, Alan C. Cheng
Step Change Improvement in ADMET Prediction with PotentialNet Deep Featurization. CoRR (2019)
Rishi Sharma, Shane T. Barratt, Stefano Ermon, Vijay S. Pande
Improved Training with Curriculum GANs. CoRR (2018)
Amir Barati Farimani, Joseph Gomes, Rishi Sharma, Franklin L. Lee, Vijay S. Pande
Deep Learning Phase Segregation. CoRR (2018)
Peter K. Eastman, Jade Shi, Bharath Ramsundar, Vijay S. Pande
Solving the RNA design problem with reinforcement learning. PLoS Comput. Biol. 14 (6) (2018)
Jade Shi, Rhiju Das, Vijay S. Pande
SentRNA: Improving computational RNA design by incorporating a prior of human design strategies. CoRR (2018)
Rishi Sharma, Amir Barati Farimani, Joe Gomes, Peter K. Eastman, Vijay S. Pande
Weakly-Supervised Deep Learning of Heat Transport via Physics Informed Loss. CoRR (2018)
Carlos X. Hernández, Mohammad M. Sultan, Vijay S. Pande
Using Deep Learning for Segmentation and Counting within Microscopy Data. CoRR (2018)
Jiaxuan You, Bowen Liu, Rex Ying, Vijay S. Pande, Jure Leskovec
Graph Convolutional Policy Network for Goal-Directed Molecular Graph Generation. CoRR (2018)
Jiaxuan You, Bowen Liu, Zhitao Ying, Vijay S. Pande, Jure Leskovec
Graph Convolutional Policy Network for Goal-Directed Molecular Graph Generation. NeurIPS (2018)
Evan N. Feinberg, Debnil Sur, Brooke E. Husic, Doris Mai, Yang Li, Jianyi Yang, Bharath Ramsundar, Vijay S. Pande
Spatial Graph Convolutions for Drug Discovery. CoRR (2018)
Hannah K. Wayment-Steele, Vijay S. Pande
Note: Variational Encoding of Protein Dynamics Benefits from Maximizing Latent Autocorrelation. CoRR (2018)
Mohammad M. Sultan, Vijay S. Pande
Decision functions from supervised machine learning algorithms as collective variables for accelerating molecular simulations. CoRR (2018)
Joseph Gomes, Bharath Ramsundar, Evan N. Feinberg, Vijay S. Pande
Atomic Convolutional Networks for Predicting Protein-Ligand Binding Affinity. CoRR (2017)
Carlos X. Hernández, Vijay S. Pande
MDEntropy: Information-Theoretic Analyses for Molecular Dynamics. J. Open Source Softw. 2 (19) (2017)
Zhenqin Wu, Bharath Ramsundar, Evan N. Feinberg, Joseph Gomes, Caleb Geniesse, Aneesh S. Pappu, Karl Leswing, Vijay S. Pande
MoleculeNet: A Benchmark for Molecular Machine Learning. CoRR (2017)
Bowen Liu, Bharath Ramsundar, Prasad Kawthekar, Jade Shi, Joseph Gomes, Quang Luu Nguyen, Stephen Ho, Jack Sloane, Paul Wender, Vijay S. Pande
Retrosynthetic reaction prediction using neural sequence-to-sequence models. CoRR (2017)
Amir Barati Farimani, Joseph Gomes, Vijay S. Pande
Deep Learning the Physics of Transport Phenomena. CoRR (2017)
Baofeng Zhang, Denise Kilburg, Peter K. Eastman, Vijay S. Pande, Emilio Gallicchio
Efficient gaussian density formulation of volume and surface areas of macromolecules on graphical processing units. J. Comput. Chem. 38 (10) (2017)
Carlos X. Hernández, Matthew P. Harrigan, Mohammad M. Sultan, Vijay S. Pande
MSMExplorer: Data Visualizations for Biomolecular Dynamics. J. Open Source Softw. 2 (12) (2017)
Peter K. Eastman, Jason M. Swails, John D. Chodera, Robert McGibbon, Yutong Zhao, Kyle Beauchamp, Lee-Ping Wang, Andrew C. Simmonett, Matthew P. Harrigan, Chaya D. Stern, Rafal P. Wiewiora, Bernard R. Brooks, Vijay S. Pande
OpenMM 7: Rapid development of high performance algorithms for molecular dynamics. PLoS Comput. Biol. 13 (7) (2017)
Bharath Ramsundar, Bowen Liu, Zhenqin Wu, Andreas Verras, Matthew Tudor, Robert P. Sheridan, Vijay S. Pande
Is Multitask Deep Learning Practical for Pharma? J. Chem. Inf. Model. 57 (8) (2017)
Steven M. Kearnes, Vijay S. Pande
ROCS-derived features for virtual screening. J. Comput. Aided Mol. Des. 30 (8) (2016)
Han Altae-Tran, Bharath Ramsundar, Aneesh S. Pappu, Vijay S. Pande
Low Data Drug Discovery with One-shot Learning. CoRR (2016)
Govindan Subramanian, Bharath Ramsundar, Vijay S. Pande, Rajiah A. Denny
Computational Modeling of β-Secretase 1 (BACE-1) Inhibitors Using Ligand Based Approaches. J. Chem. Inf. Model. 56 (10) (2016)
Bharath Ramsundar, Vijay S. Pande
Learning Protein Dynamics with Metastable Switching Systems. CoRR (2016)
Steven M. Kearnes, Kevin McCloskey, Marc Berndl, Vijay S. Pande, Patrick Riley
Molecular graph convolutions: moving beyond fingerprints. J. Comput. Aided Mol. Des. 30 (8) (2016)
Robert T. McGibbon, Carlos X. Hernández, Matthew P. Harrigan, Steven M. Kearnes, Mohammad M. Sultan, Stanislaw Jastrzebski, Brooke E. Husic, Vijay S. Pande
Osprey: Hyperparameter Optimization for Machine Learning. J. Open Source Softw. 1 (5) (2016)
Steven M. Kearnes, Kevin McCloskey, Marc Berndl, Vijay S. Pande, Patrick Riley
Molecular Graph Convolutions: Moving Beyond Fingerprints. CoRR (2016)
Bharath Ramsundar, Steven M. Kearnes, Patrick Riley, Dale Webster, David E. Konerding, Vijay S. Pande
Massively Multitask Networks for Drug Discovery. CoRR (2015)
Steven M. Kearnes, Imran S. Haque, Vijay S. Pande
SCISSORS: Practical Considerations. J. Chem. Inf. Model. 54 (1) (2014)
Robert McGibbon, Bharath Ramsundar, Mohammad Sultan, Gert Kiss, Vijay S. Pande
Understanding Protein Dynamics with L1-Regularized Reversible Hidden Markov Models. ICML (2014)
Kai J. Kohlhoff, Vijay S. Pande, Russ B. Altman
K-Means for Parallel Architectures Using All-Prefix-Sum Sorting and Updating Steps. IEEE Trans. Parallel Distributed Syst. 24 (8) (2013)
Chen Gu, Huang-Wei Chang, Lutz Maibaum, Vijay S. Pande, Gunnar E. Carlsson, Leonidas J. Guibas
Building Markov state models with solvent dynamics. BMC Bioinform. 14 (S-2) (2013)
Scott L. Delp, Joy P. Ku, Vijay S. Pande, Michael A. Sherman, Russ B. Altman
Simbios: an NIH national center for physics-based simulation of biological structures. J. Am. Medical Informatics Assoc. 19 (2) (2012)
Imran S. Haque, Vijay S. Pande
Error Bounds on the SCISSORS Approximation Method. J. Chem. Inf. Model. 51 (9) (2011)
Sander Pronk, Per Larsson, Iman Pouya, Gregory R. Bowman, Imran S. Haque, Kyle Beauchamp, Berk Hess, Vijay S. Pande, Peter M. Kasson, Erik Lindahl
Copernicus: a new paradigm for parallel adaptive molecular dynamics. SC (2011)
Imran S. Haque, Vijay S. Pande, W. Patrick Walters
Anatomy of High-Performance 2D Similarity Calculations. J. Chem. Inf. Model. 51 (9) (2011)
Kai J. Kohlhoff, Marc H. Sosnick, William T. Hsu, Vijay S. Pande, Russ B. Altman
CAMPAIGN: an open-source library of GPU-accelerated data clustering algorithms. Bioinform. 27 (16) (2011)
Peter K. Eastman, Vijay S. Pande
OpenMM: A Hardware-Independent Framework for Molecular Simulations. Comput. Sci. Eng. 12 (4) (2010)
Del Lucent, Christopher D. Snow, Colin Echeverría Aitken, Vijay S. Pande
Non-Bulk-Like Solvent Behavior in the Ribosome Exit Tunnel. PLoS Comput. Biol. 6 (10) (2010)
Imran S. Haque, Vijay S. Pande, W. Patrick Walters
SIML: A Fast SIMD Algorithm for Calculating LINGO Chemical Similarities on GPUs and CPUs. J. Chem. Inf. Model. 50 (4) (2010)
Peter K. Eastman, Vijay S. Pande
Efficient nonbonded interactions for molecular dynamics on a graphics processing unit. J. Comput. Chem. 31 (6) (2010)
Jesús A. Izaguirre, Christopher R. Sweet, Vijay S. Pande
Multiscale Dynamics of Macromolecules Using Normal Mode Langevin. Pacific Symposium on Biocomputing (2010)
Imran S. Haque, Vijay S. Pande
Hard Data on Soft Errors: A Large-Scale Assessment of Real-World Error Rates in GPGPU. CCGRID (2010)
Imran S. Haque, Vijay S. Pande
PAPER - Accelerating parallel evaluations of ROCS. J. Comput. Chem. 31 (1) (2010)
Peter M. Kasson, Erik Lindahl, Vijay S. Pande
Atomic-Resolution Simulations Predict a Transition State for Vesicle Fusion Defined by Contact of a Few Lipid Tails. PLoS Comput. Biol. 6 (6) (2010)
Imran S. Haque, Vijay S. Pande
SCISSORS: A Linear-Algebraical Technique to Rapidly Approximate Chemical Similarities. J. Chem. Inf. Model. 50 (6) (2010)
Xuhui Huang, Yuan Yao, Gregory R. Bowman, Jian Sun, Leonidas J. Guibas, Gunnar E. Carlsson, Vijay S. Pande
Constructing Multi-Resolution Markov State Models (MSMs) to Elucidate RNA Hairpin Folding Mechanisms. Pacific Symposium on Biocomputing (2010)
Peter M. Kasson, Vijay S. Pande
Cross-Graining: Efficient Multi-Scale Simulation via Markov State Models. Pacific Symposium on Biocomputing (2010)
Mark S. Friedrichs, Peter K. Eastman, Vaidyanathan Vishal, Mike Houston, Scott LeGrand, Adam L. Beberg, Daniel L. Ensign, Christopher M. Bruns, Vijay S. Pande
Accelerating molecular dynamic simulation on graphics processing units. J. Comput. Chem. 30 (6) (2009)
Imran S. Haque, Vijay S. Pande
Hard Data on Soft Errors: A Large-Scale Assessment of Real-World Error Rates in GPGPU CoRR (2009)
Peter M. Kasson, Vijay S. Pande
Combining Mutual Information with Structural Analysis to Screen for Functionally Important Residues in Influenza Hemagglutinin. Pacific Symposium on Biocomputing (2009)
Vincent A. Voelz, P. Petrone, Vijay S. Pande
A Multiscale Approach to Sampling Nascent Peptide Chains in the Ribosomal Exit Tunnel. Pacific Symposium on Biocomputing (2009)
Edgar Luttmann, Daniel L. Ensign, Vaidyanathan Vishal, Mike Houston, Noam Rimon, Jeppe Øland, Guha Jayachandran, Mark S. Friedrichs, Vijay S. Pande
Accelerating molecular dynamic simulation on the cell processor and Playstation 3. J. Comput. Chem. 30 (2) (2009)
Adam L. Beberg, Vijay S. Pande
Thalweg: A framework for programming 1, 000 machines with 1, 000 cores. IPDPS (2009)
Adam L. Beberg, Daniel L. Ensign, Guha Jayachandran, Siraj Khaliq, Vijay S. Pande
Folding@home: Lessons from eight years of volunteer distributed computing. IPDPS (2009)
Luca Monticelli, Eric J. Sorin, D. Peter Tieleman, Vijay S. Pande, Giorgio Colombo
Molecular simulation of multistate peptide dynamics: A comparison between microsecond timescale sampling and multiple shorter trajectories. J. Comput. Chem. 29 (11) (2008)
Jeanette P. Schmidt, Scott L. Delp, Michael A. Sherman, Charles A. Taylor, Vijay S. Pande, Russ B. Altman
The Simbios National Center: Systems Biology in Motion. Proc. IEEE 96 (8) (2008)
Alex Robertson, Edgar Luttmann, Vijay S. Pande
Effects of long-range electrostatic forces on simulated protein folding kinetics. J. Comput. Chem. 29 (5) (2008)
Peter M. Kasson, Vijay S. Pande
Predicting Structure and Dynamics of Loosely-Ordered Protein Complexes: Influenza Hemagglutinin Fusion Peptide. Pacific Symposium on Biocomputing (2007)
Adam L. Beberg, Vijay S. Pande
Storage@home: Petascale Distributed Storage. IPDPS (2007)
Erich Elsen, Vaidyanathan Vishal, Mike Houston, Vijay S. Pande, Pat Hanrahan, Eric Darve
N-Body Simulations on GPUs CoRR (2007)
Peter M. Kasson, Vijay S. Pande
Control of Membrane Fusion Mechanism by Lipid Composition: Predictions from Ensemble Molecular Dynamics. PLoS Comput. Biol. 3 (11) (2007)
Peter M. Kasson, Afra Zomorodian, Sanghyun Park, Nina Singhal, Leonidas J. Guibas, Vijay S. Pande
Persistent voids: a new structural metric for membrane fusion. Bioinform. 23 (14) (2007)
Erich Elsen, Mike Houston, Vaidyanathan Vishal, Eric Darve, Pat Hanrahan, Vijay S. Pande
Poster reception - N-Body simulation on GPUs. SC (2006)
Eric J. Sorin, Vijay S. Pande
Empirical force-field assessment: The interplay between backbone torsions and noncovalent term scaling. J. Comput. Chem. 26 (7) (2005)
Sanghyun Park, Randall J. Radmer, Teri E. Klein, Vijay S. Pande
A new set of molecular mechanics parameters for hydroxyproline and its use in molecular dynamics simulations of collagen-like peptides. J. Comput. Chem. 26 (15) (2005)
Peter M. Kasson, Vijay S. Pande
Computational Simulation of Lipid Bilayer Reorientation at Gaps. CSB (2003)