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

BgN-Score and BsN-Score: Bagging and boosting based ensemble neural networks scoring functions for accurate binding affinity prediction of protein-ligand complexes

(2015) Hossam M Ashtawy et al.   BMC BIOINFORMATICS

Machine-learning approaches in drug discovery: methods and applications

(2015) Antonio Lavecchia   DRUG DISCOVERY TODAY

Comparative assessment of machine-learning scoring functions on PDBbind 2013

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

A Comparative Assessment of Predictive Accuracies of Conventional and Machine Learning Scoring Functions for Protein-Ligand Binding Affinity Prediction

(2015) Hossam M. Ashtawy et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Big Data Meets Quantum Chemistry Approximations: The Δ-Machine Learning Approach

(2015) Raghunathan Ramakrishnan et al.   Journal of Chemical Theory and Computation

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

Low-Quality Structural and Interaction Data Improves Binding Affinity Prediction via Random Forest

(2015) Hongjian Li et al.   MOLECULES

Deep learning

(2015) Yann LeCun et al.   NATURE

Machine learning applications in genetics and genomics

(2015) Maxwell W. Libbrecht et al.   NATURE REVIEWS GENETICS

Optimizing the affinity and specificity of ligand binding with the inclusion of solvation effect

(2015) Zhiqiang Yan et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Machine learning: Trends, perspectives, and prospects

(2015) M. I. Jordan et al.   SCIENCE

Improved protein–ligand binding affinity prediction by using a curvature-dependent surface-area model

(2014) Yang Cao et al.   BIOINFORMATICS

Substituting random forest for multiple linear regression improves binding affinity prediction of scoring functions: Cyscore as a case study

(2014) Hongjian Li et al.   BMC BIOINFORMATICS

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

Comparative Assessment of Scoring Functions on an Updated Benchmark: 2. Evaluation Methods and General Results

(2014) Yan Li et al.   Journal of Chemical Information and Modeling

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

Comparative Assessment of Scoring Functions on an Updated Benchmark: 1. Compilation of the Test Set

(2014) Yan Li et al.   Journal of Chemical Information and Modeling

Pharmacophore-Based Similarity Scoring for DOCK

(2014) Lingling Jiang et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Drug repositioning by structure-based virtual screening

(2013) Dik-Lung Ma et al.   CHEMICAL SOCIETY REVIEWS

Virtual Screening Strategies in Drug Discovery: A Critical Review

(2013) A. Lavecchia et al.   CURRENT MEDICINAL CHEMISTRY

Binding Affinity Prediction for Protein–Ligand Complexes Based on β Contacts and B Factor

(2013) Qian Liu et al.   Journal of Chemical Information and Modeling

ID-Score: A New Empirical Scoring Function Based on a Comprehensive Set of Descriptors Related to Protein–Ligand Interactions

(2013) Guo-Bo Li et al.   Journal of Chemical Information and Modeling

SFCscoreRF: A Random Forest-Based Scoring Function for Improved Affinity Prediction of Protein–Ligand Complexes

(2013) David Zilian 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

Optimization of molecular docking scores with support vector rank regression

(2013) Wei Wang et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Structure-Based Virtual Screening for Drug Discovery: a Problem-Centric Review

(2012) Tiejun Cheng et al.   AAPS Journal

Characterization of Small Molecule Binding. I. Accurate Identification of Strong Inhibitors in Virtual Screening

(2012) Bo Ding et al.   Journal of Chemical Information and Modeling

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

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

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

Construction and Test of Ligand Decoy Sets Using MDock: Community Structure–Activity Resource Benchmarks for Binding Mode Prediction

(2011) Sheng-You Huang 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

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

Can we trust docking results? Evaluation of seven commonly used programs on PDBbind database

(2010) Dariusz Plewczynski et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Scoring functions and their evaluation methods for protein–ligand docking: recent advances and future directions

(2010) Sheng-You Huang et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Comparative Assessment of Scoring Functions on a Diverse Test Set

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

Empirical Scoring Functions for Advanced Protein−Ligand Docking with PLANTS

(2009) Oliver Korb et al.   Journal of Chemical Information and Modeling

Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit

(2008) Noel M O'Boyle et al.   Chemistry Central Journal

Virtual Screening and Its Integration with Modern Drug Design Technologies

(2008) Adriano Andricopulo et al.   CURRENT MEDICINAL CHEMISTRY

Assessment of programs for ligand binding affinity prediction

(2008) Ryangguk Kim et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY