PDBSiteScan: a program for searching for active, binding and posttranslational modification sites in the 3D structures of proteins.
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.
Ivanisenko
Vladimir A
VA
Institute of Cytology and Genetics SBRAS, Lavrentyev Avenue 10, Novosibirsk 630090, Russia.
Pintus
Sergey S
SS
Grigorovich
Dmitry A
DA
Kolchanov
Nickolay A
NA
D001665:Binding Sites; D020134:Catalytic Domain; D006867:Hydrolases / Q000737:chemistry / Q000378:metabolism; D020407:Internet; D047908:Intracellular Signaling Peptides and Proteins; D008958:Models, Molecular; D015513:Oncogene Proteins / Q000737:chemistry / Q000378:metabolism; D000071617:Protein Deglycase DJ-1; D011499:Protein Processing, Post-Translational; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism / Q000502:physiology; D012984:Software; D014584:User-Computer Interface
D047908:Intracellular Signaling Peptides and Proteins; D015513:Oncogene Proteins; D011506:Proteins; D006867:Hydrolases; C105131:PARK7 protein, human; D000071617:Protein Deglycase DJ-1