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. 2004 Jul 1;32(Web Server issue):W549-54.
doi: 10.1093/nar/gkh439.

PDBSiteScan: a program for searching for active, binding and posttranslational modification sites in the 3D structures of proteins

Vladimir A Ivanisenko  1 , Sergey S Pintus, Dmitry A Grigorovich, Nickolay A Kolchanov
Affiliations

PDBSiteScan: a program for searching for active, binding and posttranslational modification sites in the 3D structures of proteins

Vladimir A Ivanisenko et al. Nucleic Acids Res. .

Abstract

PDBSiteScan is a web-accessible program designed for searching three-dimensional (3D) protein fragments similar in structure to known active, binding and posttranslational modification sites. A collection of known sites we designated as PDBSite was set up by automated processing of the PDB database using the data on site localization in the SITE field. Additionally, protein-protein interaction sites were generated by analysis of atom coordinates in heterocomplexes. The total number of collected sites was more than 8100; they were assigned to more than 80 functional groups. PDBSiteScan provides automated search of the 3D protein fragments whose maximum distance mismatch (MDM) between N, Calpha 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. The program PDBSiteScan is available at http://wwwmgs.bionet.nsc.ru/mgs/systems/fastprot/pdbsitescan.html.

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Figures

Figure 1
Figure 1
PDBSiteScan web page.
Figure 2
Figure 2
Screen capture of the PDBSiteScan output returned to the user.
Figure 3
Figure 3
Graph showing the relation of type I (open diamonds) and type II errors (closed squares) for the catalytic site recognition in a hydrolase set to the threshold MDM values.
Figure 4
Figure 4
The results of a PDBSiteScan search demonstrate that the residues of a potential Na-binding site (stick model) of the DJ-1 protein superpose well with the real Na-binding sites (line model) of the PDBSite collection. The view of the sites was obtained using ViewerLite.
See this image and copyright information in PMC

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