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. 2011 Jul;39(Web Server issue):W235-41.
doi: 10.1093/nar/gkr437. Epub 2011 Jun 14.

firestar--advances in the prediction of functionally important residues

Gonzalo Lopez  1 , Paolo Maietta, Jose Manuel Rodriguez, Alfonso Valencia, Michael L Tress
Affiliations

firestar--advances in the prediction of functionally important residues

Gonzalo Lopez et al. Nucleic Acids Res. 2011 Jul.

Abstract

firestar is a server for predicting catalytic and ligand-binding residues in protein sequences. Here, we present the important developments since the first release of firestar. Previous versions of the server required human interpretation of the results; the server is now fully automatized. firestar has been implemented as a web service and can now be run in high-throughput mode. Prediction coverage has been greatly improved with the extension of the FireDB database and the addition of alignments generated by HHsearch. Ligands in FireDB are now classified for biological relevance. Many of the changes have been motivated by the critical assessment of techniques for protein structure prediction (CASP) ligand-binding prediction experiment, which provided us with a framework to test the performance of firestar. URL: http://firedb.bioinfo.cnio.es/Php/FireStar.php.

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Figures

Figure 1.
Figure 1.
Outstanding firestar prediction for CASP8. The prediction for target T0407, 1 of 12 targets for which firestar would have recorded the best MCC score. (A) The prediction from firestar. The residues highlighted in yellow were the prediction. (B) T0407 was a predicted metal-dependent phosphoesterase and was crystallized with three calcium atoms (shown in light green). firestar predicted all the calcium-binding residues (shown in red) without any over prediction.
Figure 2.
Figure 2.
firestar performance during CASP8. Over the CASP8 targets, firestar obtained an MCC score of 0.75 when predicting residues in contact with ligands at a distance threshold of 0.5 Å plus van der Waals distances. The figure shows the targets separated into easier and harder targets based on their homology to known structures (10). firestar had higher MCC scores than all officially participating groups in CASP8, including human predictors.
Figure 3.
Figure 3.
The new firestar interface. (A) Summary results page. In the upper part, the query amino acid sequence with predicted catalytic site residues (highlighted green residues) and binding site residues (yellow) shown on a single line. A text summary is displayed below for each prediction with a resume of the site score, the residues involved, and possible ligand if the site is ligand binding. (B) The HHsearch extended results page showing alignments between 1tcoC and two templates. The previous output style has been maintained, per-residue local conservation score is shown in blue (the darker the blue the more strong the local conservation) and the ligand-binding residues (or catalytic residues) in each FireDB template highlighted below the query-template alignment and the conservation score. (C) A PYMOL representation of the surface of PDB structure 1tcoC surface interacting with its inhibitor FK5 (‘sticks’). The residues highlighted in red represent the firestar prediction from (A). (D) A Jmol representation of the LGA structural alignment between 1tcoC and the template 1q6uA. The Jmol applet integrated in firestar permits the visualization of the binding residues and/or catalytic residues (‘sticks’) of both structures.
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