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

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

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

firestar —advances in the prediction of functionally important residues

(2011) Gonzalo Lopez et al.   NUCLEIC ACIDS RESEARCH

Assessment of ligand-binding residue predictions in CASP9

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

How significant is a protein structure similarity with TM-score = 0.5?

(2010) Jinrui Xu et al.   BIOINFORMATICS

I-TASSER: a unified platform for automated protein structure and function prediction

(2010) Ambrish Roy et al.   Nature Protocols

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

Protein structure prediction: when is it useful?

(2009) Yang Zhang   CURRENT OPINION IN STRUCTURAL BIOLOGY

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

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

Prediction of protein functional residues from sequence by probability density estimation

(2008) J. D. Fischer et al.   BIOINFORMATICS

I-TASSER server for protein 3D structure prediction

(2008) Yang Zhang   BMC BIOINFORMATICS