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

Redesign of coenzyme B12 dependent diol dehydratase to be resistant to the mechanism-based inactivation by glycerol and act on longer chain 1,2-diols

(2012) Mamoru Yamanishi et al.   FEBS Journal

FINDSITEX: A Structure-Based, Small Molecule Virtual Screening Approach with Application to All Identified Human GPCRs

(2012) Hongyi Zhou et al.   MOLECULAR PHARMACEUTICS

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

ProtChemSI: a network of protein-chemical structural interactions

(2011) O. V. Kalinina et al.   NUCLEIC ACIDS RESEARCH

Reorganizing the protein space at the Universal Protein Resource (UniProt)

(2011)   NUCLEIC ACIDS RESEARCH

The UniProt-GO Annotation database in 2011

(2011) E. C. Dimmer et al.   NUCLEIC ACIDS RESEARCH

The Gene Ontology: enhancements for 2011

(2011)   NUCLEIC ACIDS RESEARCH

KEGG for integration and interpretation of large-scale molecular data sets

(2011) M. Kanehisa et al.   NUCLEIC ACIDS RESEARCH

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

The RCSB Protein Data Bank: redesigned web site and web services

(2010) P. W. Rose et al.   NUCLEIC ACIDS RESEARCH

PepX: a structural database of non-redundant protein–peptide complexes

(2009) Peter Vanhee et al.   NUCLEIC ACIDS RESEARCH

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

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

FINDSITELHM: A Threading-Based Approach to Ligand Homology Modeling

(2009) Michal Brylinski et al.   PLoS Computational Biology

RsiteDB: a database of protein binding pockets that interact with RNA nucleotide bases

(2008) A. Shulman-Peleg et al.   NUCLEIC ACIDS RESEARCH