Beware of Simple Methods for Structure-Based Virtual Screening: The Critical Importance of Broader Comparisons

Accuracy or novelty: what can we gain from target-specific machine-learning-based scoring functions in virtual screening?

(2021) Chao Shen et al.   BRIEFINGS IN BIOINFORMATICS

Generating property-matched decoy molecules using deep learning

(2021) Fergus Imrie et al.   BIOINFORMATICS

Persistent spectral–based machine learning (PerSpect ML) for protein-ligand binding affinity prediction

(2021) Zhenyu Meng et al.   Science Advances

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

Recent progress on the prospective application of machine learning to structure-based virtual screening

(2021) Ghita Ghislat et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Virtual discovery of melatonin receptor ligands to modulate circadian rhythms

(2020) Reed M. Stein et al.   NATURE

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

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

Machine‐learning scoring functions for structure‐based virtual screening

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

The impact of compound library size on the performance of scoring functions for structure-based virtual screening

(2020) Louison Fresnais et al.   BRIEFINGS IN BIOINFORMATICS

Improving structure-based virtual screening performance via learning from scoring function components

(2020) Guo-Li Xiong et al.   BRIEFINGS IN BIOINFORMATICS

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

In silico molecular target prediction unveils mebendazole as a potent MAPK14 inhibitor

(2020) Jeremy Ariey‐Bonnet et al.   Molecular Oncology

Identification and Validation of Carbonic Anhydrase II as the First Target of the Anti-Inflammatory Drug Actarit

(2020) Ghita Ghislat et al.   Biomolecules

Classical scoring functions for docking are unable to exploit large volumes of structural and interaction data

(2019) Hongjian Li et al.   BIOINFORMATICS

From machine learning to deep learning: Advances in scoring functions for protein-ligand docking

(2019) Chao Shen et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

Improving the Virtual Screening Ability of Target-Specific Scoring Functions Using Deep Learning Methods

(2019) Dingyan Wang et al.   Frontiers in Pharmacology

MathDL: mathematical deep learning for D3R Grand Challenge 4

(2019) Duc Duy Nguyen et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

The Effect of Debiasing Protein–Ligand Binding Data on Generalization

(2019) Vikram Sundar et al.   Journal of Chemical Information and Modeling

Most Ligand-Based Classification Benchmarks Reward Memorization Rather than Generalization

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

Development of a Protein-Ligand Extended Connectivity (PLEC) fingerprint and its application for binding affinity predictions

(2018) Maciej Wójcikowski et al.   BIOINFORMATICS

Practical Model Selection for Prospective Virtual Screening

(2018) Shengchao Liu et al.   Journal of Chemical Information and Modeling

ChEMBL: towards direct deposition of bioassay data

(2018) David Mendez et al.   NUCLEIC ACIDS RESEARCH

Task-Specific Scoring Functions for Predicting Ligand Binding Poses and Affinity and for Screening Enrichment

(2017) Hossam M. Ashtawy 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

Performance of machine-learning scoring functions in structure-based virtual screening

(2017) Maciej Wójcikowski et al.   Scientific Reports

Constructing and Validating High-Performance MIEC-SVM Models in Virtual Screening for Kinases: A Better Way for Actives Discovery

(2016) Huiyong Sun et al.   Scientific Reports

Neural-Network Scoring Functions Identify Structurally Novel Estrogen-Receptor Ligands

(2015) Jacob D. Durrant et al.   Journal of Chemical Information and Modeling

Machine-learning scoring functions to improve structure-based binding affinity prediction and virtual screening

(2015) Qurrat Ul Ain et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

The Precision-Recall Plot Is More Informative than the ROC Plot When Evaluating Binary Classifiers on Imbalanced Datasets

(2015) Takaya Saito et al.   PLoS One

Integrating docking scores, interaction profiles and molecular descriptors to improve the accuracy of molecular docking: Toward the discovery of novel Akt1 inhibitors

(2014) Wenhu Zhan et al.   EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY

Evaluation and Optimization of Virtual Screening Workflows with DEKOIS 2.0 – A Public Library of Challenging Docking Benchmark Sets

(2013) Matthias R. Bauer et al.   Journal of Chemical Information and Modeling

Lessons Learned in Empirical Scoring with smina from the CSAR 2011 Benchmarking Exercise

(2013) David Ryan Koes et al.   Journal of Chemical Information and Modeling

Hierarchical virtual screening for the discovery of new molecular scaffolds in antibacterial hit identification

(2012) P. J. Ballester et al.   Journal of the Royal Society Interface

Target-Specific Support Vector Machine Scoring in Structure-Based Virtual Screening: Computational Validation, In Vitro Testing in Kinases, and Effects on Lung Cancer Cell Proliferation

(2011) Liwei Li et al.   Journal of Chemical Information and Modeling

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

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

Open Babel: An open chemical toolbox

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

A machine learning approach to predicting protein–ligand binding affinity with applications to molecular docking

(2010) Pedro J. Ballester et al.   BIOINFORMATICS

NNScore: A Neural-Network-Based Scoring Function for the Characterization of Protein−Ligand Complexes

(2010) Jacob D. Durrant et al.   Journal of Chemical Information and Modeling

Extended-Connectivity Fingerprints

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

Ultrafast shape recognition: Evaluating a new ligand-based virtual screening technology

(2009) Pedro J. Ballester et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

Prospective virtual screening with Ultrafast Shape Recognition: the identification of novel inhibitors of arylamine N-acetyltransferases

(2009) P. J. Ballester et al.   Journal of the Royal Society Interface