PDBSiteScan -- A program for searching for active, binding and posttranslational modification sites in the 3D structures of proteins
What you can do:
Search 3D protein fragments similar in structure to known active, binding and posttranslational modification sites.
Highlights:
- The collection of known sites (PDBSite) was set up by automated processing of the PDB database using the data on site localization in the SITE field.
- Additionally, proteinx96protein interaction sites were generated by analysis of atom coordinates in heterocomplexes.
- The total number of collected sites was more than 8100, assigned to more than 80 functional groups.
- PDBSiteScan provides automated search of the 3D protein fragments whose maximum distance mismatch (MDM) between N, C and C atoms in a fragment and a functional site is not larger than the MDM threshold defined by the user.
- PDBSiteScan requires perfect matching of amino acids. PDBSiteScan enables recognition of functional sites in tertiary structures of proteins and allows proteins with functional information to be annotated.
Keywords:
- protein structures
- protein 3D structures
- protein active sites
- Posttranslational modification sites
- Metal binding sites
- Inorganic nonmetal binding sites
- Organic ligand binding sites
- drug binding sites
- Protein binding sites
- DNA-binding sites
- protein functional sites
Literature & Tutorials:
PubMed Link: PDBSiteScan
This record last updated: 05-11-2005