Catalytic Site Identification

Biochemical and Biophysical
Systems Group

The catalytic site identification web server allows you to use a very fast structure-matching algorithm to search for matches between catalytic sites and proteins. You can define your own catalytic sites and match to all PDB proteins; or you can upload a protein structure file and match to all catalytic sites (from the Catalytic Site Atlas and elsewhere). In addition, you can browse our database of matches between all catalytic sites and all PDB proteins. In each case the matches can be visualized with the Jmol viewer. See: Rapid catalytic template searching as an enzyme function prediction procedure and Web server to identify catalytic sites throughout PDB

Last PDB update
2016-11-15

Find catalytic sites in PDB

Find catalytic sites in your proteins

Browse all matches

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References/data

Automated-access script

Other resources

VinaLC parallel docking

AS2TS homology modeling

User name and password

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Find your catalytic sites in PDB proteins

Define catalytic sites by specifying critical residues given in PDB files (your own PDB files, uploaded below, or from standard PDB).

Format: Comma-separated: PDB_file_id, catalytic_site_name/EC_number, residue_name|substitute|..., chain, residue_number, label (optional) More info

Catalytic-site definitions:	Format Load example data Two-catalytic-site example

Your proteins (uploaded below) will be searched, too.

Catalytic-site coordinate data

Catalytic site:	(Coordinate data file in PDB format)

Find CSA catalytic sites in your proteins

Protein:	(File in PDB format)

Browse all matches between library catalytic sites and PDB

Search by PDB ID

Search for unannotated PDB proteins by EC number

EC number:	(For example, "4.2.1" finds all that begin with "4.2.1.")

Physical and Life
Sciences Directorate

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Department of Energy's National Nuclear Security Administration.