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Vijay S. Pande
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2020 – today
- 2023
- [i22]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
OpenMM 8: Molecular Dynamics Simulation with Machine Learning Potentials. CoRR abs/2310.03121 (2023) - 2020
- [j34]Keri A. McKiernan
Dynamical model of the CLC-2 ion channel reveals conformational changes associated with selectivity-filter gating. PLoS Comput. Biol. 16(3) (2020) - [c16]Weihua Hu, Bowen Liu, Joseph Gomes, Marinka Zitnik, Percy Liang, Vijay S. Pande, Jure Leskovec:
Strategies for Pre-training Graph Neural Networks. ICLR 2020
2010 – 2019
- 2019
- [i21]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 abs/1903.11789 (2019) - [i20]Weihua Hu, Bowen Liu, Joseph Gomes, Marinka Zitnik, Percy Liang, Vijay S. Pande, Jure Leskovec:
Pre-training Graph Neural Networks. CoRR abs/1905.12265 (2019) - 2018
- [j33]Peter K. Eastman
Solving the RNA design problem with reinforcement learning. PLoS Comput. Biol. 14(6) (2018) - [c15]Jiaxuan You, Bowen Liu, Zhitao Ying, Vijay S. Pande, Jure Leskovec:
Graph Convolutional Policy Network for Goal-Directed Molecular Graph Generation. NeurIPS 2018: 6412-6422 - [i19]Mohammad M. Sultan, Vijay S. Pande:
Decision functions from supervised machine learning algorithms as collective variables for accelerating molecular simulations. CoRR abs/1802.10510 (2018) - [i18]Carlos X. Hernández, Mohammad M. Sultan, Vijay S. Pande:
Using Deep Learning for Segmentation and Counting within Microscopy Data. CoRR abs/1802.10548 (2018) - [i17]Jade Shi, Rhiju Das, Vijay S. Pande:
SentRNA: Improving computational RNA design by incorporating a prior of human design strategies. CoRR abs/1803.03146 (2018) - [i16]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 abs/1803.04465 (2018) - [i15]Hannah K. Wayment-Steele, Vijay S. Pande:
Note: Variational Encoding of Protein Dynamics Benefits from Maximizing Latent Autocorrelation. CoRR abs/1803.06449 (2018) - [i14]Amir Barati Farimani, Joseph Gomes, Rishi Sharma, Franklin L. Lee, Vijay S. Pande:
Deep Learning Phase Segregation. CoRR abs/1803.08993 (2018) - [i13]Jiaxuan You, Bowen Liu, Rex Ying, Vijay S. Pande, Jure Leskovec:
Graph Convolutional Policy Network for Goal-Directed Molecular Graph Generation. CoRR abs/1806.02473 (2018) - [i12]Rishi Sharma, Shane T. Barratt, Stefano Ermon, Vijay S. Pande:
Improved Training with Curriculum GANs. CoRR abs/1807.09295 (2018) - [i11]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 abs/1807.11374 (2018) - 2017
- [j32]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): 740-752 (2017) - [j31]Bharath Ramsundar
Is Multitask Deep Learning Practical for Pharma? J. Chem. Inf. Model. 57(8): 2068-2076 (2017) - [j30]Carlos X. Hernández
MSMExplorer: Data Visualizations for Biomolecular Dynamics. J. Open Source Softw. 2(12): 188 (2017) - [j29]Carlos X. Hernández
MDEntropy: Information-Theoretic Analyses for Molecular Dynamics. J. Open Source Softw. 2(19): 427 (2017) - [j28]Peter K. Eastman
OpenMM 7: Rapid development of high performance algorithms for molecular dynamics. PLoS Comput. Biol. 13(7) (2017) - [i10]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 abs/1703.00564 (2017) - [i9]Joseph Gomes, Bharath Ramsundar, Evan N. Feinberg, Vijay S. Pande:
Atomic Convolutional Networks for Predicting Protein-Ligand Binding Affinity. CoRR abs/1703.10603 (2017) - [i8]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 abs/1706.01643 (2017) - [i7]Amir Barati Farimani, Joseph Gomes, Vijay S. Pande:
Deep Learning the Physics of Transport Phenomena. CoRR abs/1709.02432 (2017) - 2016
- [j27]Steven Kearnes
Molecular graph convolutions: moving beyond fingerprints. J. Comput. Aided Mol. Des. 30(8): 595-608 (2016) - [j26]Steven Kearnes
ROCS-derived features for virtual screening. J. Comput. Aided Mol. Des. 30(8): 609-617 (2016) - [j25]Govindan Subramanian
Computational Modeling of β-Secretase 1 (BACE-1) Inhibitors Using Ligand Based Approaches. J. Chem. Inf. Model. 56(10): 1936-1949 (2016) - [j24]Robert T. McGibbon, Carlos X. Hernández
Osprey: Hyperparameter Optimization for Machine Learning. J. Open Source Softw. 1(5): 34 (2016) - [i6]Steven Kearnes, Kevin McCloskey, Marc Berndl, Vijay S. Pande, Patrick Riley:
Molecular Graph Convolutions: Moving Beyond Fingerprints. CoRR abs/1603.00856 (2016) - [i5]Bharath Ramsundar, Vijay S. Pande:
Learning Protein Dynamics with Metastable Switching Systems. CoRR abs/1610.01642 (2016) - [i4]Han Altae-Tran, Bharath Ramsundar, Aneesh S. Pappu, Vijay S. Pande:
Low Data Drug Discovery with One-shot Learning. CoRR abs/1611.03199 (2016) - 2015
- [i3]Bharath Ramsundar, Steven Kearnes, Patrick Riley, Dale Webster, David E. Konerding, Vijay S. Pande:
Massively Multitask Networks for Drug Discovery. CoRR abs/1502.02072 (2015) - 2014
- [j23]Steven M. Kearnes, Imran S. Haque, Vijay S. Pande:
SCISSORS: Practical Considerations. J. Chem. Inf. Model. 54(1): 5-15 (2014) - [c14]Robert McGibbon, Bharath Ramsundar, Mohammad Sultan, Gert Kiss, Vijay S. Pande:
Understanding Protein Dynamics with L1-Regularized Reversible Hidden Markov Models. ICML 2014: 1197-1205 - 2013
- [j22]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): S8 (2013) - [j21]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): 1602-1612 (2013) - 2012
- [j20]Scott L. Delp
Simbios: an NIH national center for physics-based simulation of biological structures. J. Am. Medical Informatics Assoc. 19(2): 186-189 (2012) - 2011
- [j19]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): 2321-2322 (2011) - [j18]Imran S. Haque, Vijay S. Pande:
Error Bounds on the SCISSORS Approximation Method. J. Chem. Inf. Model. 51(9): 2248-2253 (2011) - [j17]Imran S. Haque, Vijay S. Pande, W. Patrick Walters:
Anatomy of High-Performance 2D Similarity Calculations. J. Chem. Inf. Model. 51(9): 2345-2351 (2011) - [c13]Sander Pronk, Per Larsson, Iman Pouya, Gregory R. Bowman, Imran S. Haque, Kyle Beauchamp, Berk Hess
Copernicus: a new paradigm for parallel adaptive molecular dynamics. SC 2011: 60:1-60:10 - 2010
- [j16]Peter K. Eastman, Vijay S. Pande:
OpenMM: A Hardware-Independent Framework for Molecular Simulations. Comput. Sci. Eng. 12(4): 34-39 (2010) - [j15]Imran S. Haque, Vijay S. Pande:
PAPER - Accelerating parallel evaluations of ROCS. J. Comput. Chem. 31(1): 117-132 (2010) - [j14]Peter K. Eastman, Vijay S. Pande:
Efficient nonbonded interactions for molecular dynamics on a graphics processing unit. J. Comput. Chem. 31(6): 1268-1272 (2010) - [j13]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): 560-564 (2010) - [j12]Imran S. Haque, Vijay S. Pande:
SCISSORS: A Linear-Algebraical Technique to Rapidly Approximate Chemical Similarities. J. Chem. Inf. Model. 50(6): 1075-1088 (2010) - [j11]Peter M. Kasson
Atomic-Resolution Simulations Predict a Transition State for Vesicle Fusion Defined by Contact of a Few Lipid Tails. PLoS Comput. Biol. 6(6) (2010) - [j10]Del Lucent, Christopher D. Snow
Non-Bulk-Like Solvent Behavior in the Ribosome Exit Tunnel. PLoS Comput. Biol. 6(10) (2010) - [c12]Imran S. Haque, Vijay S. Pande:
Hard Data on Soft Errors: A Large-Scale Assessment of Real-World Error Rates in GPGPU. CCGRID 2010: 691-696 - [c11]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: 228-239 - [c10]Jesús A. Izaguirre, Christopher R. Sweet, Vijay S. Pande:
Multiscale Dynamics of Macromolecules Using Normal Mode Langevin. Pacific Symposium on Biocomputing 2010: 240-251 - [c9]Peter M. Kasson, Vijay S. Pande:
Cross-Graining: Efficient Multi-Scale Simulation via Markov State Models. Pacific Symposium on Biocomputing 2010: 260-268
2000 – 2009
- 2009
- [j9]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): 268-274 (2009) - [j8]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): 864-872 (2009) - [c8]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: 1-8 - [c7]Adam L. Beberg, Vijay S. Pande:
Thalweg: A framework for programming 1, 000 machines with 1, 000 cores. IPDPS 2009: 1-7 - [c6]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: 340-352 - [c5]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: 492-503 - [i2]Imran S. Haque, Vijay S. Pande:
Hard Data on Soft Errors: A Large-Scale Assessment of Real-World Error Rates in GPGPU. CoRR abs/0910.0505 (2009) - 2008
- [j7]Alex Robertson, Edgar Luttmann, Vijay S. Pande:
Effects of long-range electrostatic forces on simulated protein folding kinetics. J. Comput. Chem. 29(5): 694-700 (2008) - [j6]Luca Monticelli
Molecular simulation of multistate peptide dynamics: A comparison between microsecond timescale sampling and multiple shorter trajectories. J. Comput. Chem. 29(11): 1740-1752 (2008) - [j5]Jeanette P. Schmidt, Scott L. Delp
The Simbios National Center: Systems Biology in Motion. Proc. IEEE 96(8): 1266-1280 (2008) - 2007
- [j4]Peter M. Kasson
Persistent voids: a new structural metric for membrane fusion. Bioinform. 23(14): 1753-1759 (2007) - [j3]Peter M. Kasson
Control of Membrane Fusion Mechanism by Lipid Composition: Predictions from Ensemble Molecular Dynamics. PLoS Comput. Biol. 3(11) (2007) - [c4]Adam L. Beberg, Vijay S. Pande:
Storage@home: Petascale Distributed Storage. IPDPS 2007: 1-6 - [c3]Peter M. Kasson, Vijay S. Pande:
Predicting Structure and Dynamics of Loosely-Ordered Protein Complexes: Influenza Hemagglutinin Fusion Peptide. Pacific Symposium on Biocomputing 2007: 40-50 - [i1]Erich Elsen, Vaidyanathan Vishal, Mike Houston, Vijay S. Pande, Pat Hanrahan, Eric Darve:
N-Body Simulations on GPUs. CoRR abs/0706.3060 (2007) - 2006
- [c2]Erich Elsen, Mike Houston, Vaidyanathan Vishal, Eric Darve, Pat Hanrahan, Vijay S. Pande:
Poster reception - N-Body simulation on GPUs. SC 2006: 188 - 2005
- [j2]Eric J. Sorin, Vijay S. Pande:
Empirical force-field assessment: The interplay between backbone torsions and noncovalent term scaling. J. Comput. Chem. 26(7): 682-690 (2005) - [j1]Sanghyun Park, Randall J. Radmer, Teri E. Klein
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): 1612-1616 (2005) - 2003
- [c1]Peter M. Kasson, Vijay S. Pande:
Computational Simulation of Lipid Bilayer Reorientation at Gaps. CSB 2003: 464-467
Coauthor Index
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