Firestar server

Predicting functional residues from structural templates and alignment reliability

firestar [1,2] predicts functionally important residues. Predictions are made by evaluating internally generated alignments using SQUARE.

  • firestar runs HHsearch[3] and PSI-BLAST[4] to generate alignments.
  • Profiles are generated from a local 70% non-redundant database.
  • Alignments are generated between the target sequences and FireDB[5] templates.
  • Users may specify the e-value cut-off for the final round of the PSI-BLAST search - the default value (10) is intentionally high to mine the functional information in distantly related proteins.
  • A batch mode is available, please see the online help for more information.
  • New per-residue frequency score and per-site reliability score are available in the results page;
    Check the what's new page and the Help page for more details

Choose a query type:



ANAYSIS OF LARGE PROTEINS MAY TAKE A LONG TIME!! We recommended you provide a valid e-mail address.It may be benefical to parse large proeins into doamins before submission.


alignment tool for firestar server

The reliability of the predictions is sensitive to alignment quality and automatically generated alignments may not be the optimal alignments. This tool allows users to paste their own pairwise query-template alignments.

  • All fields are required: at present alignments should be in fasta format with the "template" sequence in the second position.
  • The template PDB code is the four letter identifier for the nearest PDB entry to the "template" sequence. If the coordinates file contains a chain identifier this must be entered too.
  • The second sequence should be in the PDB database, but in practice the tool will still work as long as there is sufficient similarity to a FireDB template.

Note that template sequence may be corrected if the sequence does not match with the one stored in the FireDB database.

More information about this tool in the online help page.


[1] firestar -- prediction of functionally important residues using structural templates and alignment reliability Lopez G, Valencia A, Tress ML.
Nucleic Acids Research, Volume 35, Issue suppl_2, 1 July 2007, Pages W573-W577;

[2] firestar -- advances in the prediction of functionally important residues Lopez G, Maietta P, Rodriguez JM, Valencia A, Tress ML.
Nucleic Acids Research, Volume 39, Issue suppl_2, 1 July 2011, Pages W235-W241;

[3] Protein homology detection by HMM–HMM comparison Söding J.
Bioinformatics, Volume 21, Issue 7, 1 April 2005, Pages 951-960; DOI:10.1093/bioinformatics/bti125

[4] Gapped BLAST and PSI-BLAST: a new generation of protein database search programs Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ.
Nucleic Acids Research, Volume 25, Issue 17, 1 September 1997, Pages 3389-3402;

[5] FireDB: a compendium of biological and pharmacologically relevant ligands Maietta P, Lopez G, Carro A, Pingilley BJ, Leon LG, Valencia A, Tress ML.
Nucleic Acids Research, Volume 42, Issue D1, 1 January 2014, Pages D267-D272

[6] FireDB -- a database of functionally important residues from proteins of known structure Lopez G, Valencia A and Tress ML.
Nucleic Acids Research, Volume 35, Issue suppl_1, 1 January 2007, Pages D219-D223;

Technical support:
Scientific support:, Gonzalo Lopez