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firestar server: predicting functional residues from structural templates and alignment reliability

*	Query type	Insert Area

	PDB code (e.g. 1zun)		Chain:


	Upload PDB coordinates file


	Fasta sequence

OPTIONS	E-value:	e-mail address:

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.

firecat: alignment tool for firestar server


Alignment
	Template PDB code:(e.g. "1q6u") Chain id:(e.g. "A")

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.

References:
1. "firestar--prediction of functionally important residues using structural templates and alignment reliability" Lopez G, Valencia A and Tress ML.
Nucleic Acids Research 2007; doi:10.1093/nar/gkm297
2. "firestar--advances in the prediction of functionally important residues" Lopez G, Maietta P, Rodriguez JM, Valencia A and Tress ML.
Nucleic Acids Research 2011; doi: 10.1093/nar/gkr437
3. "Protein homology detection by HMM-HMM comparison."Söding J.
Bioinformatics 2005; 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 and Lipman DJ.
Nucleic Acids Res 1997, 25(17), 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 2014; doi: 10.1093/nar/gkt1127
6. "FireDB--a database of functionally important residues from proteins of known structure" Lopez G, Valencia A and Tress ML.
Nucleic Acids Research 2006; doi: 10.1093/nar/gkl897

Technical support: pmaietta@cnio.es
Scientific support: mtress@cnio.es, Gonzalo Lopez