Prediction of ligand binding sites using improved blind docking method with a Machine Learning-Based scoring function

AutoDock Vina 1.2.0: New Docking Methods, Expanded Force Field, and Python Bindings

(2021) Jerome Eberhardt et al.   Journal of Chemical Information and Modeling

The AutoDock suite at 30

(2020) David S. Goodsell et al.   PROTEIN SCIENCE

Molecular Docking: Shifting Paradigms in Drug Discovery

(2019) Luca Pinzi et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

P2Rank: machine learning based tool for rapid and accurate prediction of ligand binding sites from protein structure

(2018) Radoslav Krivák et al.   Journal of Cheminformatics

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

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

Can We Rely on Computational Predictions To Correctly Identify Ligand Binding Sites on Novel Protein Drug Targets? Assessment of Binding Site Prediction Methods and a Protocol for Validation of Predicted Binding Sites

(2016) Neal K. Broomhead et al.   CELL BIOCHEMISTRY AND BIOPHYSICS

Molecular Docking and Structure-Based Drug Design Strategies

(2015) Leonardo Ferreira et al.   MOLECULES

PDB-wide collection of binding data: current status of the PDBbind database

(2014) Zhihai Liu et al.   BIOINFORMATICS

Protein–ligand binding site recognition using complementary binding-specific substructure comparison and sequence profile alignment

(2013) Jianyi Yang et al.   BIOINFORMATICS

Recognizing Protein-Ligand Binding Sites by Global Structural Alignment and Local Geometry Refinement

(2012) Ambrish Roy et al.   STRUCTURE

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

(2011) Chi-Ho Ngan et al.   BIOINFORMATICS

Open Babel: An open chemical toolbox

(2011) Noel M O'Boyle et al.   Journal of Cheminformatics

3DLigandSite: predicting ligand-binding sites using similar structures

(2010) Mark N. Wass et al.   NUCLEIC ACIDS RESEARCH

Fpocket: An open source platform for ligand pocket detection

(2009) Vincent Le Guilloux et al.   BMC BIOINFORMATICS

AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility

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

Predicting Protein Ligand Binding Sites by Combining Evolutionary Sequence Conservation and 3D Structure

(2009) John A. Capra et al.   PLoS Computational Biology

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

(2002) Csaba Hetényi et al.   PROTEIN SCIENCE