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FireDB is a database of Protein Data Bank structures, ligands and annotated functional site residues. The database can be accessed by PDB codes or UniProt accession numbers as well as keywords.
firestar predicts functionally important residues based on the FireDB database. The predictions are based on the local evaluation of alignments between the query sequence and the structures with functional information that are stored in FireDB. firestar allows many alignment formats, including pairwise alignments with PSI-BLAST and HHsearch, multiple alignments with MUSCLE and structural alignments with LGA. Users can even input their own alignments. The reliability of predictions is assessed with SQUARE and the functional information is highlighted along with a reliability score. Users can make queries with sequences and alignments or upload PDB structures.
Ligand info

FireDB contains information on every chemical compound in the PDB, including their descriptions, the PDB structures in which the compounds are found and the amino acids that are in contact with the ligand.


The Server for Quick Alignment Reliability Evaluation is a Web-based version of the method we developed to predict regions of reliably aligned residues in sequence alignments. Given an alignment between a query sequence and a sequence of known structure, SQUARE is able to predict which residues are reliably aligned. This is a stand alone implementation of the version included in firestar.


For a more detailed description.
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Additional tools:

The Ligand Contact Tool (LCT)
LCT is a tool to calculate contacts between protein and ligand atoms in known structures. Several parameters are available (distance cut-off, Van Der Waals radii usage, etc).

    Authors:           Gonzalo Lopez, Alfonso Valencia & Michael L. Tress
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