EDock: blind protein–ligand docking by replica-exchange monte carlo simulation

DockRMSD: an open-source tool for atom mapping and RMSD calculation of symmetric molecules through graph isomorphism

(2019) Eric W. Bell et al.   Journal of Cheminformatics

LS-align: an atom-level, flexible ligand structural alignment algorithm for high-throughput virtual screening

(2018) Jun Hu et al.   BIOINFORMATICS

DOCK 6: Impact of new features and current docking performance

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

The I-TASSER Suite: protein structure and function prediction

(2015) Jianyi Yang et al.   NATURE METHODS

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

(2013) Jianyi Yang et al.   BIOINFORMATICS

Directory of Useful Decoys, Enhanced (DUD-E): Better Ligands and Decoys for Better Benchmarking

(2012) Michael M. Mysinger et al.   JOURNAL OF MEDICINAL CHEMISTRY

BioLiP: a semi-manually curated database for biologically relevant ligand–protein interactions

(2012) Jianyi Yang et al.   NUCLEIC ACIDS RESEARCH

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

(2012) Ambrish Roy et al.   STRUCTURE

Assessment of ligand-binding residue predictions in CASP9

(2011) Tobias Schmidt et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

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

Conformer Generation with OMEGA: Algorithm and Validation Using High Quality Structures from the Protein Databank and Cambridge Structural Database

(2010) Paul C. D. Hawkins et al.   Journal of Chemical Information and Modeling

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

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

Predicting Small-Molecule Solvation Free Energies: An Informal Blind Test for Computational Chemistry

(2008) Anthony Nicholls et al.   JOURNAL OF MEDICINAL CHEMISTRY