Vijay S. Pande

CoRR, 2018

Spatial Graph Convolutions for Drug Discovery.

[BibT_eX]

[DOI]

CoRR, 2018

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

[BibT_eX]

[DOI]

Jade Shi

Rhiju Das

CoRR, 2018

Using Deep Learning for Segmentation and Counting within Microscopy Data.

[BibT_eX]

[DOI]

Carlos X. Hernández

Mohammad M. Sultan

CoRR, 2018

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

[BibT_eX]

[DOI]

Mohammad M. Sultan

CoRR, 2018

Graph Convolutional Policy Network for Goal-Directed Molecular Graph Generation.

[BibT_eX]

[DOI]

Proceedings of the Advances in Neural Information Processing Systems 31: Annual Conference on Neural Information Processing Systems 2018, 2018

2017

Is Multitask Deep Learning Practical for Pharma?

[BibT_eX]

[DOI]

J. Chem. Inf. Model., August, 2017

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

[BibT_eX]

[DOI]

PLoS Comput. Biol., 2017

MDEntropy: Information-Theoretic Analyses for Molecular Dynamics.

[BibT_eX]

[DOI]

Carlos X. Hernández

J. Open Source Softw., 2017

MSMExplorer: Data Visualizations for Biomolecular Dynamics.

[BibT_eX]

[DOI]

J. Open Source Softw., 2017

Efficient gaussian density formulation of volume and surface areas of macromolecules on graphical processing units.

[BibT_eX]

[DOI]

J. Comput. Chem., 2017

Deep Learning the Physics of Transport Phenomena.

[BibT_eX]

[DOI]

Amir Barati Farimani

Joseph Gomes

CoRR, 2017

MoleculeNet: A Benchmark for Molecular Machine Learning.

[BibT_eX]

[DOI]

CoRR, 2017

Retrosynthetic reaction prediction using neural sequence-to-sequence models.

[BibT_eX]

[DOI]

CoRR, 2017

Atomic Convolutional Networks for Predicting Protein-Ligand Binding Affinity.

[BibT_eX]

[DOI]

CoRR, 2017

2016

Osprey: Hyperparameter Optimization for Machine Learning.

[BibT_eX]

[DOI]

Stanislaw Jastrzebski

Brooke E. Husic

J. Open Source Softw., 2016

Computational Modeling of β-Secretase 1 (BACE-1) Inhibitors Using Ligand Based Approaches.

[BibT_eX]

[DOI]

J. Chem. Inf. Model., 2016

ROCS-derived features for virtual screening.

[BibT_eX]

[DOI]

Steven Kearnes

J. Comput. Aided Mol. Des., 2016

Molecular graph convolutions: moving beyond fingerprints.

[BibT_eX]

[DOI]

J. Comput. Aided Mol. Des., 2016

Learning Protein Dynamics with Metastable Switching Systems.

[BibT_eX]

[DOI]

Bharath Ramsundar

CoRR, 2016

Low Data Drug Discovery with One-shot Learning.

[BibT_eX]

[DOI]

CoRR, 2016

2015

Massively Multitask Networks for Drug Discovery.

[BibT_eX]

[DOI]

CoRR, 2015

2014

SCISSORS: Practical Considerations.

[BibT_eX]

[DOI]

Steven M. Kearnes

J. Chem. Inf. Model., 2014

Understanding Protein Dynamics with L1-Regularized Reversible Hidden Markov Models.

[BibT_eX]

[DOI]

Proceedings of the 31th International Conference on Machine Learning, 2014

2013

K-Means for Parallel Architectures Using All-Prefix-Sum Sorting and Updating Steps.

[BibT_eX]

[DOI]

Kai J. Kohlhoff

Russ B. Altman

IEEE Trans. Parallel Distributed Syst., 2013

Building Markov state models with solvent dynamics.

[BibT_eX]

[DOI]

BMC Bioinform., 2013

2012

Simbios: an NIH national center for physics-based simulation of biological structures.

[BibT_eX]

[DOI]

J. Am. Medical Informatics Assoc., 2012

2011

Anatomy of High-Performance 2D Similarity Calculations.

[BibT_eX]

[DOI]

W. Patrick Walters

J. Chem. Inf. Model., 2011

Error Bounds on the SCISSORS Approximation Method.

[BibT_eX]

[DOI]

J. Chem. Inf. Model., 2011

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

[BibT_eX]

[DOI]

Bioinform., 2011

Copernicus: a new paradigm for parallel adaptive molecular dynamics.

[BibT_eX]

[DOI]

Proceedings of the Conference on High Performance Computing Networking, 2011

2010

Non-Bulk-Like Solvent Behavior in the Ribosome Exit Tunnel.

[BibT_eX]

[DOI]

Del Lucent

Christopher D. Snow

Colin Echeverría Aitken

PLoS Comput. Biol., 2010

Atomic-Resolution Simulations Predict a Transition State for Vesicle Fusion Defined by Contact of a Few Lipid Tails.

[BibT_eX]

[DOI]

Erik Lindahl

PLoS Comput. Biol., 2010

SIML: A Fast SIMD Algorithm for Calculating LINGO Chemical Similarities on GPUs and CPUs.

[BibT_eX]

[DOI]

W. Patrick Walters

J. Chem. Inf. Model., 2010

SCISSORS: A Linear-Algebraical Technique to Rapidly Approximate Chemical Similarities.

[BibT_eX]

[DOI]

J. Chem. Inf. Model., 2010

PAPER - Accelerating parallel evaluations of ROCS.

[BibT_eX]

[DOI]

J. Comput. Chem., 2010

Efficient nonbonded interactions for molecular dynamics on a graphics processing unit.

[BibT_eX]

[DOI]

Peter K. Eastman

J. Comput. Chem., 2010

OpenMM: A Hardware-Independent Framework for Molecular Simulations.

[BibT_eX]

[DOI]

Peter K. Eastman

Comput. Sci. Eng., 2010

Cross-Graining: Efficient Multi-Scale Simulation via Markov State Models.

[BibT_eX]

[DOI]

Proceedings of the Biocomputing 2010: Proceedings of the Pacific Symposium, 2010

Multiscale Dynamics of Macromolecules Using Normal Mode Langevin.

[BibT_eX]

[DOI]

Jesús A. Izaguirre

Christopher R. Sweet

Proceedings of the Biocomputing 2010: Proceedings of the Pacific Symposium, 2010

Constructing Multi-Resolution Markov State Models (MSMs) to Elucidate RNA Hairpin Folding Mechanisms.

[BibT_eX]

[DOI]

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.

[BibT_eX]

[DOI]

Proceedings of the 10th IEEE/ACM International Conference on Cluster, 2010

2009

Accelerating molecular dynamic simulation on the cell processor and Playstation 3.

[BibT_eX]

[DOI]

J. Comput. Chem., 2009

Accelerating molecular dynamic simulation on graphics processing units.

[BibT_eX]

[DOI]

J. Comput. Chem., 2009

A Multiscale Approach to Sampling Nascent Peptide Chains in the Ribosomal Exit Tunnel.

[BibT_eX]

[DOI]

Vincent A. Voelz

P. Petrone

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.

[BibT_eX]

[DOI]

Proceedings of the Biocomputing 2009: Proceedings of the Pacific Symposium, 2009

Thalweg: A framework for programming 1, 000 machines with 1, 000 cores.

[BibT_eX]

[DOI]

Adam L. Beberg

Proceedings of the 23rd IEEE International Symposium on Parallel and Distributed Processing, 2009

Folding@home: Lessons from eight years of volunteer distributed computing.

[BibT_eX]

[DOI]

Proceedings of the 23rd IEEE International Symposium on Parallel and Distributed Processing, 2009

2008

The Simbios National Center: Systems Biology in Motion.

[BibT_eX]

[DOI]

Proc. IEEE, 2008

Effects of long-range electrostatic forces on simulated protein folding kinetics.

[BibT_eX]

[DOI]

Alex Robertson

Edgar Luttmann

J. Comput. Chem., 2008

Molecular simulation of multistate peptide dynamics: A comparison between microsecond timescale sampling and multiple shorter trajectories.

[BibT_eX]

[DOI]

J. Comput. Chem., 2008

2007

Control of Membrane Fusion Mechanism by Lipid Composition: Predictions from Ensemble Molecular Dynamics.

[BibT_eX]

[DOI]

PLoS Comput. Biol., 2007

N-Body Simulations on GPUs

[BibT_eX]

[DOI]

CoRR, 2007

Persistent voids: a new structural metric for membrane fusion.

[BibT_eX]

[DOI]

Bioinform., 2007

Predicting Structure and Dynamics of Loosely-Ordered Protein Complexes: Influenza Hemagglutinin Fusion Peptide.

[BibT_eX]

[DOI]

Proceedings of the Biocomputing 2007, 2007

Storage@home: Petascale Distributed Storage.

[BibT_eX]

[DOI]

Adam L. Beberg

Proceedings of the 21th International Parallel and Distributed Processing Symposium (IPDPS 2007), 2007

2006

Poster reception - N-Body simulation on GPUs.

[BibT_eX]

[DOI]

Proceedings of the ACM/IEEE SC2006 Conference on High Performance Networking and Computing, 2006

2005

Empirical force-field assessment: The interplay between backbone torsions and noncovalent term scaling.

[BibT_eX]

[DOI]

Eric J. Sorin

J. Comput. Chem., 2005

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

[BibT_eX]

[DOI]

J. Comput. Chem., 2005

2003

Computational Simulation of Lipid Bilayer Reorientation at Gaps.

[BibT_eX]

[DOI]