Vijay S. Pande

Cultivating Health Care’s AI Future

Vijay S. Pande, Arjun Kumar Manrai, Andrew L. Beam

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OpenMM 8: Molecular Dynamics Simulation with Machine Learning Potentials

Peter K. Eastman, Raimondas Galvelis, Raúl P. Peláez, Charlles R. A. Abreu et autres

Machine learning plays an important and growing role in molecular simulation. The newest version of the OpenMM molecular dynamics toolkit introduces new features to support the use of machine learning potentials. Arbitrary PyTorch models can be added to a simulation and used …

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OpenMM 8: Molecular Dynamics Simulation with Machine Learning Potentials

Peter K. Eastman, Raimondas Galvelis, Raúl P. Peláez, Charlles R. A. Abreu et autres

Machine learning plays an important and growing role in molecular simulation. The newest version of the OpenMM molecular dynamics toolkit introduces new features to support the use of machine learning potentials. Arbitrary PyTorch models can be added to a simulation and used …

Folding@home: Achievements from over 20 years of citizen science herald the exascale era

Vincent A. Voelz, Vijay S. Pande, Gregory R. Bowman

Simulations of biomolecules have enormous potential to inform our understanding of biology but require extremely demanding calculations. For over twenty years, the Folding@home distributed computing project has pioneered a massively parallel approach to biomolecular simulation, harnessing the resources of citizen scientists across …

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Folding@home: achievements from over twenty years of citizen science herald the exascale era

Vincent A. Voelz, Vijay S. Pande, Gregory R. Bowman

Simulations of biomolecules have enormous potential to inform our understanding of biology but require extremely demanding calculations. For over twenty years, the Folding@home distributed computing project has pioneered a massively parallel approach to biomolecular simulation, harnessing the resources of citizen scientists across …

Monteggia Fracture Bado III

Samir S. Shah, Vijay S. Pande

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Computational IR Spectroscopy of Insulin Dimer Structure and Conformational Heterogeneity

Chi-Jui Feng, Anton V. Sinitskiy, Vijay S. Pande, Andrei Tokmakoff

We have investigated the structure and conformational dynamics of insulin dimer using a Markov state model (MSM) built from extensive unbiased atomistic molecular dynamics simulations and performed infrared spectral simulations of the insulin MSM to describe how structural variation within the dimer …

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Computational IR Spectroscopy of Insulin Dimer Structure and Conformational Heterogeneity

Chi-Jui Feng, Anton V. Sinitskiy, Vijay S. Pande, Andrei Tokmakoff

We have investigated the structure and conformational dynamics of insulin dimer using a Markov state model (MSM) built from extensive unbiased atomistic MD simulations, and performed infrared spectral simulations of the insulin MSM to describe how structural variation within the dimer can …

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Computational IR Spectroscopy of Insulin Dimer Structure and Conformational Heterogeneity

Chi-Jui Feng, Anton V. Sinitskiy, Vijay S. Pande, Andrei Tokmakoff

We have investigated the structure and conformational dynamics of insulin dimer using a Markov state model (MSM) built from extensive unbiased atomistic MD simulations, and performed infrared spectral simulations of the insulin MSM to describe how structural variation within the dimer can …

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A Targeted Computational Screen of the SWEETLEAD Database Reveals FDA-Approved Compounds with Anti-Dengue Viral Activity

Jasmine Moshiri, David A. Constant, Bowen Liu, Roberto Mateo et autres

No antiviral therapeutics are currently available for dengue virus infections. By computationally overlaying the three-dimensional (3D) chemical structures of compounds known to inhibit dengue virus over those of compounds known to be safe in humans, we identified three FDA-approved compounds that are …

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A targeted computational screen of the SWEETLEAD database reveals FDA-approved compounds with anti-dengue viral activity

Jasmine Moshiri, David A. Constant, Bowen Liu, Roberto Mateo et autres

Abstract Affordable and effective antiviral therapies are needed worldwide, especially against agents such as dengue virus that are endemic in underserved regions. Many antiviral compounds have been studied in cultured cells but are unsuitable for clinical applications due to pharmacokinetic profiles, side …

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Improvement in ADMET Prediction with Multitask Deep Featurization

Evan N. Feinberg, Elizabeth Joshi, Vijay S. Pande, Alan C. Cheng

The absorption, distribution, metabolism, elimination, and toxicity (ADMET) properties of drug candidates are important for their efficacy and safety as therapeutics. Predicting ADMET properties has therefore been of great interest to the computational chemistry and medicinal chemistry communities in recent decades. Traditional …

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