Recognizing metal and acid radical ion-binding sites by integratingab initiomodeling with template-based transferals

The I-TASSER Suite: protein structure and function prediction

(2015) Jianyi Yang et al.   NATURE METHODS

LigandRFs: random forest ensemble to identify ligand-binding residues from sequence information alone

(2014) Peng Chen et al.   BMC BIOINFORMATICS

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

(2013) Jianyi Yang et al.   BIOINFORMATICS

Designing Template-Free Predictor for Targeting Protein-Ligand Binding Sites with Classifier Ensemble and Spatial Clustering

(2013) Dong-Jun Yu et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

The Protein Model Portal—a comprehensive resource for protein structure and model information

(2013) Juergen Haas et al.   Database-The Journal of Biological Databases and Curation

A comparative assessment and analysis of 20 representative sequence alignment methods for protein structure prediction

(2013) Renxiang Yan et al.   Scientific Reports

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

(2012) Jianyi Yang et al.   NUCLEIC ACIDS RESEARCH

COFACTOR: an accurate comparative algorithm for structure-based protein function annotation

(2012) Ambrish Roy et al.   NUCLEIC ACIDS RESEARCH

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

(2012) Ambrish Roy et al.   STRUCTURE

LIBSVM

(2012) Chih-Chung Chang et al.   ACM Transactions on Intelligent Systems and Technology

FunFOLD: an improved automated method for the prediction of ligand binding residues using 3D models of proteins

(2011) Daniel B Roche et al.   BMC BIOINFORMATICS

Assessment of ligand-binding residue predictions in CASP9

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

3DLigandSite: predicting ligand-binding sites using similar structures

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

Protein interactions and ligand binding: From protein subfamilies to functional specificity

(2010) A. Rausell et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

ANGLOR: A Composite Machine-Learning Algorithm for Protein Backbone Torsion Angle Prediction

(2008) Sitao Wu et al.   PLoS One