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

A Deep Learning Approach to Antibiotic Discovery

(2020) Jonathan M. Stokes et al.   CELL

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

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

Virtual screening web servers: designing chemical probes and drug candidates in the cyberspace

(2020) Natesh Singh et al.   BRIEFINGS IN BIOINFORMATICS

Ultra-large library docking for discovering new chemotypes

(2019) Jiankun Lyu et al.   NATURE

Improved Method of Structure-Based Virtual Screening via Interaction-Energy-Based Learning

(2019) Nobuaki Yasuo et al.   Journal of Chemical Information and Modeling

The next level in chemical space navigation: going far beyond enumerable compound libraries

(2019) Torsten Hoffmann et al.   DRUG DISCOVERY TODAY

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

(2019) Hongjian Li et al.   BIOINFORMATICS

Concepts of Artificial Intelligence for Computer-Assisted Drug Discovery

(2019) Xin Yang et al.   CHEMICAL REVIEWS

AGL-Score: Algebraic Graph Learning Score for Protein–Ligand Binding Scoring, Ranking, Docking, and Screening

(2019) Duc Duy Nguyen et al.   Journal of Chemical Information and Modeling

Taba: A Tool to Analyze the Binding Affinity

(2019) Amauri Duarte da Silva et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

DLIGAND2: an improved knowledge-based energy function for protein–ligand interactions using the distance-scaled, finite, ideal-gas reference state

(2019) Pin Chen et al.   Journal of Cheminformatics

Learning from the ligand: using ligand-based features to improve binding affinity prediction

(2019) Fergus Boyles et al.   BIOINFORMATICS

Application of Machine Learning Techniques to Predict Binding Affinity for Drug Targets. A Study of Cyclin-Dependent Kinase 2

(2019) Gabriela Bitencourt-Ferreira et al.   CURRENT MEDICINAL CHEMISTRY

Incorporating Explicit Water Molecules and Ligand Conformation Stability in Machine-Learning Scoring Functions

(2019) Jianing Lu et al.   Journal of Chemical Information and Modeling

MathDL: mathematical deep learning for D3R Grand Challenge 4

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

Virtual Screening in Hepatitis B Virus Drug Discovery: Current Stateof- the-Art and Future Perspectives

(2018) Mohcine Elmessaoudi-Idrissi et al.   CURRENT MEDICINAL CHEMISTRY

Machine Learning Classification Models to Improve the Docking-based Screening: A Case of PI3K-Tankyrase Inhibitors

(2018) Vladimir P. Berishvili et al.   Molecular Informatics

Mathematical deep learning for pose and binding affinity prediction and ranking in D3R Grand Challenges

(2018) Duc Duy Nguyen et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Online structure-based screening of purchasable approved drugs and natural compounds: retrospective examples of drug repositioning on cancer targets

(2018) Nathalie Lagarde et al.   Oncotarget

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

Protein–Ligand Empirical Interaction Components for Virtual Screening

(2017) Yuna Yan et al.   Journal of Chemical Information and Modeling

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

Correcting the impact of docking pose generation error on binding affinity prediction

(2016) Hongjian Li et al.   BMC BIOINFORMATICS

Effect of Binding Pose and Modeled Structures on SVMGen and GlideScore Enrichment of Chemical Libraries

(2016) David Xu et al.   Journal of Chemical Information and Modeling

The ChEMBL database in 2017

(2016) Anna Gaulton et al.   NUCLEIC ACIDS RESEARCH

USR-VS: a web server for large-scale prospective virtual screening using ultrafast shape recognition techniques

(2016) Hongjian Li et al.   NUCLEIC ACIDS RESEARCH

Rocker: Open source, easy-to-use tool for AUC and enrichment calculations and ROC visualization

(2016) Sakari Lätti et al.   Journal of Cheminformatics

Benchmark of four popular virtual screening programs: construction of the active/decoy dataset remains a major determinant of measured performance

(2016) Ludovic Chaput et al.   Journal of Cheminformatics

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

Building a virtual ligand screening pipeline using free software: a survey

(2015) Enrico Glaab   BRIEFINGS IN BIOINFORMATICS

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

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

Hierarchical virtual screening approaches in small molecule drug discovery

(2015) Ashutosh Kumar et al.   METHODS

Improving AutoDock Vina Using Random Forest: The Growing Accuracy of Binding Affinity Prediction by the Effective Exploitation of Larger Data Sets

(2015) Hongjian Li et al.   Molecular Informatics

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

Does a More Precise Chemical Description of Protein–Ligand Complexes Lead to More Accurate Prediction of Binding Affinity?

(2014) Pedro J. Ballester et al.   Journal of Chemical Information and Modeling

Improvement of Virtual Screening Results by Docking Data Feature Analysis

(2014) Marcelino Arciniega et al.   Journal of Chemical Information and Modeling

The holistic integration of virtual screening in drug discovery

(2013) Yusuf Tanrikulu et al.   DRUG DISCOVERY TODAY

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

Consensus Docking: Improving the Reliability of Docking in a Virtual Screening Context

(2013) Douglas R. Houston 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

Ligand Pose and Orientational Sampling in Molecular Docking

(2013) Ryan G. Coleman et al.   PLoS One

Directory of Useful Decoys, Enhanced (DUD-E): Better Ligands and Decoys for Better Benchmarking

(2012) Michael M. Mysinger et al.   JOURNAL OF MEDICINAL CHEMISTRY

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

Global Analysis of Small Molecule Binding to Related Protein Targets

(2012) Felix A. Kruger et al.   PLoS Computational Biology

Structure-Based Virtual Screening Approach to the Discovery of Novel Inhibitors of Eyes Absent 2 Phosphatase with Various Metal Chelating Moieties

(2011) Hwangseo Park et al.   Chemical Biology & Drug Design

Support Vector Regression Scoring of Receptor–Ligand Complexes for Rank-Ordering and Virtual Screening of Chemical Libraries

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

Discovery of Potent Inhibitors of Soluble Epoxide Hydrolase by Combinatorial Library Design and Structure-Based Virtual Screening

(2011) Li Xing et al.   JOURNAL OF MEDICINAL CHEMISTRY

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

(2010) Pedro J. Ballester et al.   BIOINFORMATICS

Virtual screening: an endless staircase?

(2010) Gisbert Schneider   NATURE REVIEWS DRUG DISCOVERY

Fpocket: An open source platform for ligand pocket detection

(2009) Vincent Le Guilloux et al.   BMC BIOINFORMATICS

Mining free compound databases to identify candidates selected by virtual screening

(2009) Sridhar R Vasudevan et al.   Expert Opinion on Drug Discovery

Comparative Assessment of Scoring Functions on a Diverse Test Set

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

Experimental Approaches to Evaluate the Thermodynamics of Protein- Drug Interactions

(2008) Walter de Azevedo Jr. et al.   CURRENT DRUG TARGETS