firestar server: predicting functional residues from structural templates and alignment reliabilityfirestar [1] predicts functionally important residues. Predictions are made by evaluating internally generated alignments using SQUARE. User supplied target sequences (including those with known structures) are first subjected to PSI-BLAST search of the PDB. PSI-BLAST generates its profiles with a locally generated 90% redundant database. The final search is against the fireDB template database. Users may specify the e-value cut-off for the search of the fireDB templates; note that the default value (10) is intentionally high as functional information may be present in even very distantly related proteins. There are two further alignment options, it is possible to generate multiple sequence alignments with the templates found by PSI-BLAST using MUSCLE and to generate structural alignments between query and template structures with LGA [2]. See the online help for more information on firestar. |
| Query type | Insert Area | Chain | E-value | Submission |  |
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firecat: alignment tool for firestar serverThe reliability of the predictions is sensitive to alignment quality and automatically generated PSI-BLAST 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. See the online help for more information about this tool. |
1. FireDB--a database of functionally important residues from proteins of known structure. Gonzalo Lopez; A. Valencia; M. Tress Nucleic Acids Research 2006; doi: 10.1093/nar/gkl897
2. firestar--prediction of functionally important residues using structural templates and alignment reliability. Gonzalo Lopez; A. Valencia; M. Tress Nucleic Acids Research, doi:10.1093/nar/gkm297
3. LGA: A method for finding 3D similarities in protein structures. Zemla A. Nucleic Acids Res. 2003 Jul 1;31(13):3370-4.
Technical support: glopez@cnio.es
Scientifical support: glopez@cnio.es, mtress@cnio.es