Improving Blind Docking in DOCK6 through an Automated Preliminary Fragment Probing Strategy

CB-Dock: a web server for cavity detection-guided protein–ligand blind docking

(2019) Yang Liu et al.   ACTA PHARMACOLOGICA SINICA

Key Topics in Molecular Docking for Drug Design

(2019) Pedro H. M. Torres et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

CavityPlus: a web server for protein cavity detection with pharmacophore modelling, allosteric site identification and covalent ligand binding ability prediction

(2018) Youjun Xu et al.   NUCLEIC ACIDS RESEARCH

COACH-D: improved protein–ligand binding sites prediction with refined ligand-binding poses through molecular docking

(2018) Qi Wu et al.   NUCLEIC ACIDS RESEARCH

Protein-Ligand Blind Docking Using QuickVina-W With Inter-Process Spatio-Temporal Integration

(2017) Nafisa M. Hassan et al.   Scientific Reports

DOCK 6: Impact of new features and current docking performance

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

The FTMap family of web servers for determining and characterizing ligand-binding hot spots of proteins

(2015) Dima Kozakov et al.   Nature Protocols

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

A dynamic niching genetic algorithm strategy for docking highly flexible ligands

(2014) Camila Silva de Magalhães et al.   INFORMATION SCIENCES

pocketZebra: a web-server for automated selection and classification of subfamily-specific binding sites by bioinformatic analysis of diverse protein families

(2014) Dmitry Suplatov et al.   NUCLEIC ACIDS RESEARCH

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

(2012) A. Volkamer et al.   BIOINFORMATICS

FTSite: high accuracy detection of ligand binding sites on unbound protein structures

(2011) Chi-Ho Ngan et al.   BIOINFORMATICS

Fast docking using the CHARMM force field with EADock DSS

(2011) Aurélien Grosdidier et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

SwissDock, a protein-small molecule docking web service based on EADock DSS

(2011) A. Grosdidier et al.   NUCLEIC ACIDS RESEARCH

BSP-SLIM: A blind low-resolution ligand-protein docking approach using predicted protein structures

(2011) Hui Sun Lee et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Fpocket: An open source platform for ligand pocket detection

(2009) Vincent Le Guilloux et al.   BMC BIOINFORMATICS

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

Improving accuracy and efficiency of blind protein-ligand docking by focusing on predicted binding sites

(2008) Dario Ghersi et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Efficient docking of peptides to proteins without prior knowledge of the binding site

(2002) Csaba Hetényi et al.   PROTEIN SCIENCE