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

Accelerating AutoDock4 with GPUs and Gradient-Based Local Search

(2021) Diogo Santos-Martins et al.   Journal of Chemical Theory and Computation

Lean-Docking: Exploiting Ligands’ Predicted Docking Scores to Accelerate Molecular Docking

(2021) Francois Berenger et al.   Journal of Chemical Information and Modeling

Design of SARS-CoV-2 PLpro Inhibitors for COVID-19 Antiviral Therapy Leveraging Binding Cooperativity

(2021) Zhengnan Shen et al.   JOURNAL OF MEDICINAL CHEMISTRY

A practical guide to large-scale docking

(2021) Brian J. Bender et al.   Nature Protocols

Virtual discovery of melatonin receptor ligands to modulate circadian rhythms

(2020) Reed M. Stein et al.   NATURE

Rapid Identification of Potential Inhibitors of SARS‐CoV‐2 Main Protease by Deep Docking of 1.3 Billion Compounds

(2020) Anh-Tien Ton et al.   Molecular Informatics

An open-source drug discovery platform enables ultra-large virtual screens

(2020) Christoph Gorgulla et al.   NATURE

Deep Docking: A Deep Learning Platform for Augmentation of Structure Based Drug Discovery

(2020) Francesco Gentile et al.   ACS Central Science

Recent progress on cheminformatics approaches to epigenetic drug discovery

(2020) Zoe Sessions et al.   DRUG DISCOVERY TODAY

Emulating Docking Results Using a Deep Neural Network: A New Perspective for Virtual Screening

(2020) Stanisław Jastrzębski et al.   Journal of Chemical Information and Modeling

Generating multibillion chemical space of readily accessible screening compounds

(2020) Oleksandr O. Grygorenko et al.   iScience

Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19

(2020) A. Acharya et al.   Journal of Chemical Information and Modeling

Ultra-large library docking for discovering new chemotypes

(2019) Jiankun Lyu et al.   NATURE

Efficient iterative virtual screening with Apache Spark and conformal prediction

(2018) Laeeq Ahmed et al.   Journal of Cheminformatics

Improving Screening Efficiency through Iterative Screening Using Docking and Conformal Prediction

(2017) Fredrik Svensson et al.   Journal of Chemical Information and Modeling

Fast, accurate, and reliable molecular docking with QuickVina 2

(2015) Amr Alhossary et al.   BIOINFORMATICS

ZINC 15 – Ligand Discovery for Everyone

(2015) Teague Sterling et al.   Journal of Chemical Information and Modeling

Ambit-Tautomer: An Open Source Tool for Tautomer Generation

(2013) Nikolay T. Kochev et al.   Molecular Informatics

Docking and scoring with ICM: the benchmarking results and strategies for improvement

(2012) Marco A. C. Neves et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

FRED Pose Prediction and Virtual Screening Accuracy

(2011) Mark McGann   Journal of Chemical Information and Modeling

Open Babel: An open chemical toolbox

(2011) Noel M O'Boyle et al.   Journal of Cheminformatics

Conformer Generation with OMEGA: Algorithm and Validation Using High Quality Structures from the Protein Databank and Cambridge Structural Database

(2010) Paul C. D. Hawkins et al.   Journal of Chemical Information and Modeling

Extended-Connectivity Fingerprints

(2010) David Rogers et al.   Journal of Chemical Information and Modeling