The transformational role of GPU computing and deep learning in drug discovery

M Pandey, M Fernandez, F Gentile, O Isayev… - Nature Machine …, 2022 - nature.com
Deep learning has disrupted nearly every field of research, including those of direct
importance to drug discovery, such as medicinal chemistry and pharmacology. This …

Artificial intelligence–enabled virtual screening of ultra-large chemical libraries with deep docking

F Gentile, JC Yaacoub, J Gleave, M Fernandez… - Nature …, 2022 - nature.com
With the recent explosion of chemical libraries beyond a billion molecules, more efficient
virtual screening approaches are needed. The Deep Docking (DD) platform enables up to …

Uncertainty quantification in classical molecular dynamics

S Wan, RC Sinclair… - … Transactions of the …, 2021 - royalsocietypublishing.org
Molecular dynamics simulation is now a widespread approach for understanding complex
systems on the atomistic scale. It finds applications from physics and chemistry to …

The globus compute dataset: An open function-as-a-service dataset from the edge to the cloud

A Bauer, H Pan, R Chard, Y Babuji, J Bryan… - Future Generation …, 2024 - Elsevier
We present a unique function-as-a-service (FaaS) dataset capturing the use of the Globus
Compute (previously funcX) platform. Globus Compute implements a federated model via …

AI-coupled HPC workflow applications, middleware and performance

W Brewer, A Gainaru, F Suter, F Wang… - arxiv preprint arxiv …, 2024 - arxiv.org
AI integration is revolutionizing the landscape of HPC simulations, enhancing the
importance, use, and performance of AI-driven HPC workflows. This paper surveys the …

Frontiers in scientific workflows: Pervasive integration with high-performance computing

RF Da Silva, RM Badia, D Bard, IT Foster, S Jha… - Computer, 2024 - ieeexplore.ieee.org
We address the increasing complexity of scientific workflows in the context of high-
performance computing (HPC) and their associated need for robust, adaptable, and flexible …

Large scale study of ligand–protein relative binding free energy calculations: actionable predictions from statistically robust protocols

AP Bhati, PV Coveney - Journal of Chemical Theory and …, 2022 - ACS Publications
The accurate and reliable prediction of protein–ligand binding affinities can play a central
role in the drug discovery process as well as in personalized medicine. Of considerable …

Long time scale ensemble methods in molecular dynamics: Ligand–protein interactions and allostery in SARS-CoV-2 targets

AP Bhati, A Hoti, A Potterton, MK Bieniek… - Journal of Chemical …, 2023 - ACS Publications
We subject a series of five protein–ligand systems which contain important SARS-CoV-2
targets, 3-chymotrypsin-like protease (3CLPro), papain-like protease, and adenosine ribose …

Pre‐exascale HPC approaches for molecular dynamics simulations. Covid‐19 research: A use case

M Wieczor, V Genna, J Aranda… - Wiley …, 2023 - Wiley Online Library
Exascale computing has been a dream for ages and is close to becoming a reality that will
impact how molecular simulations are being performed, as well as the quantity and quality of …