COFACTOR is a structure-based method for biological function
annotation of protein molecules.
To use COFACTOR, user needs to provide a 3D-structural model of
the protein of interest.
COFACTOR will thread the structure through the
BioLiP protein funtion database
by local and global structure matches to identify
functional sites and homologies.
Functional insights, including ligand-binding site, gene-ontology terms, and
enzyme classification, will be
derived from the best functional homology template.
The COFACTOR algorithm was ranked as the best method for function prediction
in the community-wide
held in 2010.
Questions about the COFACTOR server can be posted at the
Service System Discussion Board
For a given target structure, the output of COFACTOR includes
(see an illustrative example
- The top 10 closest structures in the PDB searched by TM-align
- Enzyme classification of the target protein and the top 5 enzyme homologs in the PDB
- Gene Ontology (GO) terms associated with the target protein
- Possible binding ligands and the ligand-protein complex structures
- Ambrish Roy, Jianyi Yang, and Yang Zhang.
COFACTOR: An accurate comparative algorithm for structure-based protein function annotation.
Nucleic Acids Research, 40:W471-W477 (2012). (download the PDF file)
- Ambrish Roy, Yang Zhang.
Recognizing protein-ligand binding sites by global
structural alignment and local geometry refinement.
Structure, 20: 987-997 (2012)
(download the PDF file and
Jianyi Yang, Ambrish Roy, and Yang Zhang.
BioLiP: a semi-manually curated database for biologically relevant ligand-protein interactions.
Nucleic Acids Research, 41: D1096-D1103 (2013)
(download the PDF file).