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