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

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

(2014) Yang Cao et al.   BIOINFORMATICS

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

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

istar: A Web Platform for Large-Scale Protein-Ligand Docking

(2014) Hongjian Li et al.   PLoS One

aCSM: noise-free graph-based signatures to large-scale receptor-based ligand prediction

(2013) Douglas E. V. Pires et al.   BIOINFORMATICS

Drug repositioning by structure-based virtual screening

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

Scoring Functions for Prediction of Protein-Ligand Interactions

(2013) Jui-Chih Wang et al.   CURRENT PHARMACEUTICAL DESIGN

The holistic integration of virtual screening in drug discovery

(2013) Yusuf Tanrikulu et al.   DRUG DISCOVERY TODAY

Comparing Neural-Network Scoring Functions and the State of the Art: Applications to Common Library Screening

(2013) Jacob D. Durrant et al.   Journal of Chemical Information and Modeling

HotLig: A Molecular Surface-Directed Approach to Scoring Protein–Ligand Interactions

(2013) Sheng-Hung Wang 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

Latest developments in molecular docking: 2010-2011 in review

(2013) Elizabeth Yuriev et al.   JOURNAL OF MOLECULAR RECOGNITION

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

(2012) Tiejun Cheng et al.   AAPS Journal

DoGSiteScorer: a web server for automatic binding site prediction, analysis and druggability assessment

(2012) A. Volkamer et al.   BIOINFORMATICS

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

A consistent description of HYdrogen bond and DEhydration energies in protein–ligand complexes: methods behind the HYDE scoring function

(2012) Nadine Schneider et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Bioinformatics and variability in drug response: a protein structural perspective

(2012) J. L. Lahti et al.   Journal of the Royal Society Interface

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

Novel Computational Approaches to Polypharmacology as a Means to Define Responses to Individual Drugs

(2011) Lei Xie et al.   Annual Review of Pharmacology and Toxicology

CSAR Scoring Challenge Reveals the Need for New Concepts in Estimating Protein–Ligand Binding Affinity

(2011) Fedor N. Novikov 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

Robust Scoring Functions for Protein–Ligand Interactions with Quantum Chemical Charge Models

(2011) Jui-Chih Wang et al.   Journal of Chemical Information and Modeling

Comments on “Leave-Cluster-Out Cross-Validation Is Appropriate for Scoring Functions Derived from Diverse Protein Data Sets”: Significance for the Validation of Scoring Functions

(2011) Pedro J. Ballester et al.   Journal of Chemical Information and Modeling

A Machine Learning-Based Method To Improve Docking Scoring Functions and Its Application to Drug Repurposing

(2011) Sarah L. Kinnings 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

DSX: A Knowledge-Based Scoring Function for the Assessment of Protein–Ligand Complexes

(2011) Gerd Neudert et al.   Journal of Chemical Information and Modeling

Statistical Potential for Modeling and Ranking of Protein–Ligand Interactions

(2011) Hao Fan et al.   Journal of Chemical Information and Modeling

PHOENIX: A Scoring Function for Affinity Prediction Derived Using High-Resolution Crystal Structures and Calorimetry Measurements

(2011) Yat T. Tang et al.   Journal of Chemical Information and Modeling

BINANA: A novel algorithm for ligand-binding characterization

(2011) Jacob D. Durrant et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

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

(2010) Pedro J. Ballester et al.   BIOINFORMATICS

Druggable pockets and binding site centric chemical space: a paradigm shift in drug discovery

(2010) Stéphanie Pérot et al.   DRUG DISCOVERY TODAY

Binding Affinity Prediction with Property-Encoded Shape Distribution Signatures

(2010) Sourav Das et al.   Journal of Chemical Information and Modeling

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

Leave-Cluster-Out Cross-Validation Is Appropriate for Scoring Functions Derived from Diverse Protein Data Sets

(2010) Christian Kramer 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

Prediction of protein–ligand binding affinity by free energy simulations: assumptions, pitfalls and expectations

(2010) Julien Michel et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Non-additivity of Functional Group Contributions in Protein–Ligand Binding: A Comprehensive Study by Crystallography and Isothermal Titration Calorimetry

(2010) Bernhard Baum et al.   JOURNAL OF MOLECULAR BIOLOGY

Structure-Based Approaches to Target Fishing and Ligand Profiling

(2010) Didier Rognan   Molecular Informatics

Virtual screening: an endless staircase?

(2010) Gisbert Schneider   NATURE REVIEWS DRUG DISCOVERY

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

Efficient Drug Lead Discovery and Optimization

(2009) William L. Jorgensen   ACCOUNTS OF CHEMICAL RESEARCH

Comparative Assessment of Scoring Functions on a Diverse Test Set

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

AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility

(2009) Garrett M. Morris et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY