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FireDB

FireDB is a fully automated search system for structures in the Protein Data Bank, that contain annotations of residues participating in a functional site. The Database can be accessed by PDB codes or UniProt accession numbers.

The sources of functional residues are protein-ligand atom contacts and the Catalytic Site Atlas
The whole PDB was clustered at 97% sequence identity and every chain mapped onto a consensus sequence from the cluster, so that important positions can be mapped and binding sites collapsed into the consensus sequence. Comparison of binding sites within a cluster of sequences gives an idea of the flexibility of those regions and the capability they have to bind different ligand analogs.

A deteiled description of FireDB output in the FireDB online help.

firestar

firestar obtains predictions based on PSI-BLAST and HHsearch alignments against DB template database, reliability of predictions is assesed with SQUARE method and displayed in a readable manner. PSI-BLAST and HHsearch hits are used to obtain Multiple Sequence Alignment with MUSCLE, functional information is highlighted in the alignment.

A detailed description of the functionalities and methods of firestar is available in the firestar online help.

Ligand Info

Every ligand compound in the PDB is stored in tables with its chemical description, the PDB structures in which it is present and the amino acids pre-calculated to be in contact with the ligand.
This aditional feature allows ligand searches using a three letter code as well as keywords that match on chemical name or synonyms. All chemical information including the three letter code comes from the mmCIF dictionaries

What's new

In this page you can find the time registry of all changes, updates and improvements were made to FireDB and firestar server.


Additional tools:

The Ligand Contact Tool (LCT)

LCT is a tool to calculate contacts between protein residues and ligand atoms.

A PDB format file can be scanned, queries acepted are uploadable PDB format file or PDB accession code. Several parameters are available:
     Atom restriction: alpha carbon, beta carbon or all atom
     Distance constraints: use or non use of Van der Waals and the distance cutoff. When Van der Waals is checked, the sum of Van der Waals and distance is used.
Output returns: ligand names, residues in contact and the corresponding structural visualization.

    Authors:           Gonzalo Lopez, Alfonso Valencia & Michael L. Tress
    Contact mail:    pmaietta@cnio.es