Vijay S. Pande

72 papers A* 3A 5B 1Misc 6Journal 56Unranked 1

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