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

General Purpose Structure-Based Drug Discovery Neural Network Score Functions with Human-Interpretable Pharmacophore Maps

(2021) Benjamin P. Brown et al.   Journal of Chemical Information and Modeling

D3R grand challenge 4: blind prediction of protein–ligand poses, affinity rankings, and relative binding free energies

(2020) Conor D. Parks et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Machine‐learning scoring functions for structure‐based drug lead optimization

(2020) Hongjian Li et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

LIT-PCBA: An Unbiased Data Set for Machine Learning and Virtual Screening

(2020) Viet-Khoa Tran-Nguyen et al.   Journal of Chemical Information and Modeling

Structure- and Ligand-Based Virtual Screening on DUD-E+: Performance Dependence on Approximations to the Binding Pocket

(2020) Ann E. Cleves 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

D3R Grand Challenge 3: blind prediction of protein–ligand poses and affinity rankings

(2019) Zied Gaieb et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Ultra-large library docking for discovering new chemotypes

(2019) Jiankun Lyu et al.   NATURE

In Need of Bias Control: Evaluating Chemical Data for Machine Learning in Structure-Based Virtual Screening

(2019) Jochen Sieg et al.   Journal of Chemical Information and Modeling

The Light and Dark Sides of Virtual Screening: What Is There to Know?

(2019) Aleix Gimeno et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Concepts of Artificial Intelligence for Computer-Assisted Drug Discovery

(2019) Xin Yang et al.   CHEMICAL REVIEWS

Key Topics in Molecular Docking for Drug Design

(2019) Pedro H. M. Torres et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Molecular Docking: Shifting Paradigms in Drug Discovery

(2019) Luca Pinzi et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Continuous Evaluation of Ligand Protein Predictions: A Weekly Community Challenge for Drug Docking

(2019) Jeffrey R. Wagner et al.   STRUCTURE

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

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

Ensemble Docking in Drug Discovery

(2018) Rommie E. Amaro et al.   BIOPHYSICAL JOURNAL

Most Ligand-Based Classification Benchmarks Reward Memorization Rather than Generalization

(2018) Izhar Wallach et al.   Journal of Chemical Information and Modeling

Inhibition of neuronal FLT3 receptor tyrosine kinase alleviates peripheral neuropathic pain in mice

(2018) Cyril Rivat et al.   Nature Communications

Empirical Scoring Functions for Structure-Based Virtual Screening: Applications, Critical Aspects, and Challenges

(2018) Isabella A. Guedes et al.   Frontiers in Pharmacology

Protein Family-Specific Models Using Deep Neural Networks and Transfer Learning Improve Virtual Screening and Highlight the Need for More Data

(2018) Fergus Imrie et al.   Journal of Chemical Information and Modeling

Comparative Assessment of Scoring Functions: The CASF-2016 Update

(2018) Minyi Su et al.   Journal of Chemical Information and Modeling

Protein–Ligand Scoring with Convolutional Neural Networks

(2017) Matthew Ragoza et al.   Journal of Chemical Information and Modeling

Ranking docking poses by graph matching of protein–ligand interactions: lessons learned from the D3R Grand Challenge 2

(2017) Priscila da Silva Figueiredo Celestino Gomes et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

D3R Grand Challenge 2: blind prediction of protein–ligand poses, affinity rankings, and relative binding free energies

(2017) Zied Gaieb et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Boosting Docking-Based Virtual Screening with Deep Learning

(2016) Janaina Cruz Pereira et al.   Journal of Chemical Information and Modeling

Improving scoring-docking-screening powers of protein-ligand scoring functions using random forest

(2016) Cheng Wang et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Docking pose selection by interaction pattern graph similarity: application to the D3R grand challenge 2015

(2016) Inna Slynko et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

D3R grand challenge 2015: Evaluation of protein–ligand pose and affinity predictions

(2016) Symon Gathiaka et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Comparative assessment of machine-learning scoring functions on PDBbind 2013

(2015) Mohamed A. Khamis et al.   ENGINEERING APPLICATIONS OF ARTIFICIAL INTELLIGENCE

Novel aminotetrazole derivatives as selective STAT3 non-peptide inhibitors

(2015) Jean-René Pallandre et al.   EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY

Accurate and Reliable Prediction of Relative Ligand Binding Potency in Prospective Drug Discovery by Way of a Modern Free-Energy Calculation Protocol and Force Field

(2015) Lingle Wang et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

PDB-wide collection of binding data: current status of the PDBbind database

(2014) Zhihai Liu et al.   BIOINFORMATICS

Beware of Machine Learning-Based Scoring Functions—On the Danger of Developing Black Boxes

(2014) Joffrey Gabel et al.   Journal of Chemical Information and Modeling

Encoding Protein–Ligand Interaction Patterns in Fingerprints and Graphs

(2013) Jérémy Desaphy et al.   Journal of Chemical Information and Modeling

Structure-Based Discovery of Allosteric Modulators of Two Related Class B G-Protein-Coupled Receptors

(2011) Chris de Graaf et al.   ChemMedChem

CSAR Benchmark Exercise of 2010: Selection of the Protein–Ligand Complexes

(2011) James B. Dunbar et al.   Journal of Chemical Information and Modeling

Crystal Structure-Based Virtual Screening for Fragment-like Ligands of the Human Histamine H1Receptor

(2011) Chris de Graaf et al.   JOURNAL OF MEDICINAL CHEMISTRY

Estrogen Receptor Alpha as a Key Target of Red Wine Polyphenols Action on the Endothelium

(2010) Matthieu Chalopin et al.   PLoS One

Comparative Assessment of Scoring Functions on a Diverse Test Set

(2009) Tiejun Cheng et al.   Journal of Chemical Information and Modeling

AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading

(2009) Oleg Trott et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Assessment of Scaffold Hopping Efficiency by Use of Molecular Interaction Fingerprints

(2008) Jennifer Venhorst et al.   JOURNAL OF MEDICINAL CHEMISTRY

Selective Structure-Based Virtual Screening for Full and Partial Agonists of the β2 Adrenergic Receptor

(2008) Chris de Graaf et al.   JOURNAL OF MEDICINAL CHEMISTRY