Machine Learning-Enabled Pipeline for Large-Scale Virtual Drug Screening

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

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

True Accuracy of Fast Scoring Functions to Predict High-Throughput Screening Data from Docking Poses: The Simpler the Better

(2021) Viet-Khoa Tran-Nguyen et al.   Journal of Chemical Information and Modeling

Benchmarking the Ability of Common Docking Programs to Correctly Reproduce and Score Binding Modes in SARS-CoV-2 Protease Mpro

(2021) Shani Zev et al.   Journal of Chemical Information and Modeling

ChemBioServer 2.0: an advanced web server for filtering, clustering and networking of chemical compounds facilitating both drug discovery and repurposing

(2020) Evangelos Karatzas et al.   BIOINFORMATICS

Current Trends, Overlooked Issues, and Unmet Challenges in Virtual Screening

(2020) Dagmar Stumpfe et al.   Journal of Chemical Information and Modeling

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

(2020) Christoph Gorgulla et al.   NATURE

Extending the Applicability of the ANI Deep Learning Molecular Potential to Sulfur and Halogens

(2020) Christian Devereux et al.   Journal of Chemical Theory and Computation

Machine learning classification can reduce false positives in structure-based virtual screening

(2020) Yusuf O. Adeshina et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Integrating Machine Learning-Based Virtual Screening With Multiple Protein Structures and Bio-Assay Evaluation for Discovery of Novel GSK3β Inhibitors

(2020) Jingyu Zhu et al.   Frontiers in Pharmacology

Ultra-large library docking for discovering new chemotypes

(2019) Jiankun Lyu et al.   NATURE

OnionNet: a Multiple-Layer Intermolecular-Contact-Based Convolutional Neural Network for Protein–Ligand Binding Affinity Prediction

(2019) Liangzhen Zheng et al.   ACS Omega

Development and evaluation of a deep learning model for protein–ligand binding affinity prediction

(2018) Marta M Stepniewska-Dziubinska et al.   BIOINFORMATICS

Protein structure-based drug design: from docking to molecular dynamics

(2018) Paweł Śledź et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Applying Pose Clustering and MD Simulations To Eliminate False Positives in Molecular Docking

(2018) Spandana Makeneni et al.   Journal of Chemical Information and Modeling

NAMD goes quantum: an integrative suite for hybrid simulations

(2018) Marcelo C R Melo et al.   NATURE METHODS

Computational Studies on the Inhibitor Selectivity of Human JAMM Deubiquitinylases Rpn11 and CSN5

(2018) Vikash Kumar et al.   Frontiers in Chemistry

Exploring the Stability of Ligand Binding Modes to Proteins by Molecular Dynamics Simulations: A Cross-docking Study

(2017) Kai Liu et al.   Journal of Chemical Information and Modeling

Capzimin is a potent and specific inhibitor of proteasome isopeptidase Rpn11

(2017) Jing Li et al.   Nature Chemical Biology

CaFE: a tool for binding affinity prediction using end-point free energy methods

(2016) Hui Liu et al.   BIOINFORMATICS

Docking Screens for Novel Ligands Conferring New Biology

(2016) John J. Irwin et al.   JOURNAL OF MEDICINAL CHEMISTRY

Integrated machine learning, molecular docking and 3D-QSAR based approach for identification of potential inhibitors of trypanosomal N-myristoyltransferase

(2016) Nidhi Singh et al.   Molecular BioSystems

Computational protein–ligand docking and virtual drug screening with the AutoDock suite

(2016) Stefano Forli et al.   Nature Protocols

An atomic structure of the human 26S proteasome

(2016) Xiuliang Huang et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

RCD+: Fast loop modeling server

(2016) José Ramón López-Blanco et al.   NUCLEIC ACIDS RESEARCH

Targeted inhibition of the COP9 signalosome for treatment of cancer

(2016) Anita Schlierf et al.   Nature Communications

An atomic structure of the human 26S proteasome

(2016) Xiuliang Huang et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

ZINC 15 – Ligand Discovery for Everyone

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

Beware of docking!

(2015) Yu-Chian Chen   TRENDS IN PHARMACOLOGICAL SCIENCES

Structure of the Rpn11–Rpn8 dimer reveals mechanisms of substrate deubiquitination during proteasomal degradation

(2014) Evan J Worden et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Insights into the regulation of the human COP9 signalosome catalytic subunit, CSN5/Jab1

(2013) Aude Echalier et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

NNScore 2.0: A Neural-Network Receptor–Ligand Scoring Function

(2011) Jacob D. Durrant et al.   Journal of Chemical Information and Modeling

SwissParam: A fast force field generation tool for small organic molecules

(2011) Vincent Zoete et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Open Babel: An open chemical toolbox

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

PaDEL-descriptor: An open source software to calculate molecular descriptors and fingerprints

(2010) Chun Wei Yap   JOURNAL OF COMPUTATIONAL CHEMISTRY

Virtual screening: an endless staircase?

(2010) Gisbert Schneider   NATURE REVIEWS DRUG DISCOVERY

Automatic clustering of docking poses in virtual screening process using self-organizing map

(2009) Guillaume Bouvier et al.   BIOINFORMATICS

High-Performance Drug Discovery: Computational Screening by Combining Docking and Molecular Dynamics Simulations

(2009) Noriaki Okimoto et al.   PLoS Computational Biology