Pande, Vijay S.

MoleculeNet: a benchmark for molecular machine learning

Wu, Z., Ramsundar, B., Feinberg, E. N., Gomes, J., Geniesse, C., Pappu, A. S., Leswing, K., & Pande, V. (2018) · Chemical Science

Computational Drug Discovery MethodsMachine Learning in Materials Science

Cited by 3,107

OpenMM 7: Rapid development of high performance algorithms for molecular dynamics

Eastman, P., Swails, J., Chodera, J. D., McGibbon, R. T., Zhao, Y., Beauchamp, K. A., Wang, L.-P., Simmonett, A. C., Harrigan, M. P., Stern, C. D., et al. (2017) · PLOS Computational Biology

Parallel Computing and Optimization TechniquesProtein Structure and Dynamics

Cited by 2,748

Molecular graph convolutions: moving beyond fingerprints

Kearnes, S., McCloskey, K., Berndl, M., Pande, V., & Riley, P. (2016) · Journal of Computer-Aided Molecular Design

Computational Drug Discovery MethodsMachine Learning in Materials Science

Cited by 1,631

Current Status of the AMOEBA Polarizable Force Field

Ponder, J. W., Wu, C., Ren, P., Pande, V. S., Chodera, J. D., Schnieders, M. J., Haque, I., Mobley, D. L., Lambrecht, D. S., DiStasio, R. A., et al. (2010) · The Journal of Physical Chemistry B

Advanced Chemical Physics StudiesAdvanced Physical and Chemical Molecular Interactions

Cited by 1,440

Low Data Drug Discovery with One-Shot Learning

Altae-Tran, H., Ramsundar, B., Pappu, A. S., & Pande, V. (2017) · ACS Central Science

Computational Drug Discovery MethodsMachine Learning in Materials Science

Cited by 799

Everything you wanted to know about Markov State Models but were afraid to ask

Pande, V. S., Beauchamp, K., & Bowman, G. R. (2010) · Methods

Protein Structure and DynamicsAdvanced Physical and Chemical Molecular Interactions

Cited by 698

Improvements in Markov State Model Construction Reveal Many Non-Native Interactions in the Folding of NTL9

Schwantes, C. R., & Pande, V. S. (2013) · Journal of Chemical Theory and Computation

Protein Structure and DynamicsAdvanced Physical and Chemical Molecular Interactions

Cited by 597

Retrosynthetic Reaction Prediction Using Neural Sequence-to-Sequence Models

Liu, B., Ramsundar, B., Kawthekar, P., Shi, J., Gomes, J., Luu Nguyen, Q., Ho, S., Sloane, J., Wender, P., & Pande, V. (2017) · ACS Central Science

Computational Drug Discovery MethodsMachine Learning in Materials Science

Cited by 536

To milliseconds and beyond: challenges in the simulation of protein folding

Lane, T. J., Shukla, D., Beauchamp, K. A., & Pande, V. S. (2013) · Current Opinion in Structural Biology

Protein Structure and DynamicsRNA and protein synthesis mechanisms

Cited by 409

Progress and challenges in the automated construction of Markov state models for full protein systems

Bowman, G. R., Beauchamp, K. A., Boxer, G., & Pande, V. S. (2009) · The Journal of Chemical Physics

Protein Structure and DynamicsAdvanced Physical and Chemical Molecular Interactions

Cited by 396

MSMBuilder2: Modeling Conformational Dynamics on the Picosecond to Millisecond Scale

Beauchamp, K. A., Bowman, G. R., Lane, T. J., Maibaum, L., Haque, I. S., & Pande, V. S. (2011) · Journal of Chemical Theory and Computation

Protein Structure and DynamicsAdvanced Physical and Chemical Molecular Interactions

Cited by 372

Activation pathway of Src kinase reveals intermediate states as targets for drug design

Shukla, D., Meng, Y., Roux, B., & Pande, V. S. (2014) · Nature Communications

Protein Structure and DynamicsProtein Kinase Regulation and GTPase Signaling

Cited by 333

Heteropolymer freezing and design: Towards physical models of protein folding

Pande, V. S., Grosberg, A. Y., & Tanaka, T. (2000) · Reviews of Modern Physics

Protein Structure and DynamicsTheoretical and Computational Physics

Cited by 284

MSMBuilder: Statistical Models for Biomolecular Dynamics

Harrigan, M. P., Sultan, M. M., Hernández, C. X., Husic, B. E., Eastman, P., Schwantes, C. R., Beauchamp, K. A., McGibbon, R. T., & Pande, V. S. (2016) · Biophysical Journal

Protein Structure and DynamicsAdvanced Physical and Chemical Molecular Interactions

Cited by 277

MSMBuilder: Statistical Models for Biomolecular Dynamics

Harrigan, M. P., Sultan, M. M., Hernández, C. X., Husic, B. E., Eastman, P., Schwantes, C. R., Beauchamp, K. A., McGibbon, R. T., & Pande, V. S. (2017) · Biophysical Journal

Protein Structure and DynamicsAdvanced Physical and Chemical Molecular Interactions

Cited by 277

Is Multitask Deep Learning Practical for Pharma?

Ramsundar, B., Liu, B., Wu, Z., Verras, A., Tudor, M., Sheridan, R. P., & Pande, V. (2017) · Journal of Chemical Information and Modeling

Computational Drug Discovery MethodsMachine Learning in Materials Science

Cited by 263

Simple few-state models reveal hidden complexity in protein folding

Beauchamp, K. A., McGibbon, R., Lin, Y.-S., & Pande, V. S. (2012) · Proceedings of the National Academy of Sciences

Protein Structure and DynamicsRNA and protein synthesis mechanisms

Cited by 161

Atomic convolutional networks for predicting protein-ligand binding affinity

Gomes, J., Ramsundar, B., Feinberg, E. N., & Pande, V. S. (2017) · arXiv

Computational Drug Discovery MethodsMachine Learning in Bioinformatics

Cited by 150

Slow Unfolded-State Structuring in Acyl-CoA Binding Protein Folding Revealed by Simulation and Experiment

Voelz, V. A., Jäger, M., Yao, S., Chen, Y., Zhu, L., Waldauer, S. A., Bowman, G. R., Friedrichs, M., Bakajin, O., Lapidus, L. J., et al. (2012) · Journal of the American Chemical Society

Protein Structure and DynamicsRNA and protein synthesis mechanisms

Cited by 140

Finding Our Way in the Dark Proteome

Bhowmick, A., Brookes, D. H., Yost, S. R., Dyson, H. J., Forman-Kay, J. D., Gunter, D., Head-Gordon, M., Hura, G. L., Pande, V. S., Wemmer, D. E., et al. (2016) · Journal of the American Chemical Society

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 128

Investigating How Peptide Length and a Pathogenic Mutation Modify the Structural Ensemble of Amyloid Beta Monomer

Lin, Y.-S., Bowman, G. R., Beauchamp, K. A., & Pande, V. S. (2012) · Biophysical Journal

Alzheimer's disease research and treatmentsProtein Structure and Dynamics

Cited by 111

Structural Insight into RNA Hairpin Folding Intermediates

Bowman, G. R., Huang, X., Yao, Y., Sun, J., Carlsson, G., Guibas, L. J., & Pande, V. S. (2008) · Journal of the American Chemical Society

RNA and protein synthesis mechanismsProtein Structure and Dynamics

Cited by 101

Dynamical reweighting: Improved estimates of dynamical properties from simulations at multiple temperatures

Chodera, J. D., Swope, W. C., Noé, F., Prinz, J.-H., Shirts, M. R., & Pande, V. S. (2011) · The Journal of Chemical Physics

Advanced Physical and Chemical Molecular InteractionsProtein Structure and Dynamics

Cited by 71

Towards simple kinetic models of functional dynamics for a kinase subfamily

Sultan, M. M., Kiss, G., & Pande, V. (2017) · Nature Chemistry

Protein Structure and DynamicsProtein Kinase Regulation and GTPase Signaling

Cited by 68