GalaxyDock BP2 score: a hybrid scoring function for accurate protein–ligand docking

FlexAID: Revisiting Docking on Non-Native-Complex Structures

(2015) Francis Gaudreault et al.   Journal of Chemical Information and Modeling

DOCK 6: Impact of new features and current docking performance

(2015) William J. Allen et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

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

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

Protein Loop Modeling Using a New Hybrid Energy Function and Its Application to Modeling in Inaccurate Structural Environments

(2014) Hahnbeom Park et al.   PLoS One

GalaxyDock2: Protein-ligand docking using beta-complex and global optimization

(2013) Woong-Hee Shin et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

GalaxyDock: Protein–Ligand Docking with Flexible Protein Side-chains

(2012) Woong-Hee Shin et al.   Journal of Chemical Information and Modeling

Surflex-Dock: Docking benchmarks and real-world application

(2012) Russell Spitzer et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Are predefined decoy sets of ligand poses able to quantify scoring function accuracy?

(2012) Oliver Korb et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Refinement of Unreliable Local Regions in Template-based Protein Models

(2012) Hahnbeom Park et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

FRED Pose Prediction and Virtual Screening Accuracy

(2011) Mark McGann   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

LigDockCSA: Protein-ligand docking using conformational space annealing

(2011) Woong-Hee Shin et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Refinement of protein termini in template-based modeling using conformational space annealing

(2011) Hahnbeom Park et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Consistent refinement of submitted models at CASP using a knowledge-based potential

(2010) Gaurav Chopra et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

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

Comparison of Several Molecular Docking Programs: Pose Prediction and Virtual Screening Accuracy

(2009) Jason B. Cross 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

AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility

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

Medicinal Chemistry and the Molecular Operating Environment (MOE): Application of QSAR and Molecular Docking to Drug Discovery

(2008) Santiago Vilar et al.   CURRENT TOPICS IN MEDICINAL CHEMISTRY

Protein−Ligand Docking against Non-Native Protein Conformers

(2008) Marcel L. Verdonk et al.   Journal of Chemical Information and Modeling

Molecular docking with multi-objective Particle Swarm Optimization

(2007) Stefan Janson et al.   APPLIED SOFT COMPUTING