firestar--prediction of functionally important residues using structural templates and alignment reliability

Abstract

Here we present firestar, an expert system for predicting ligand-binding residues in protein structures. The server provides a method for extrapolating from the large inventory of functionally important residues organized in the FireDB database and adds information about the local conservation of potential-binding residues. The interface allows users to make queries by protein sequence or structure. The user can access pairwise and multiple alignments with structures that have relevant functionally important binding sites. The results are presented in a series of easy to read displays that allow users to compare binding residue conservation across homologous proteins. The binding site residues can also be viewed with molecular visualization tools. One feature of firestar is that it can be used to evaluate the biological relevance of small molecule ligands present in PDB structures. With the server it is easy to discern whether small molecule binding is conserved in homologous structures. We found this facility particularly useful during the recent assessment of CASP7 function prediction.

Availability: http://firedb.bioinfo.cnio.es/Php/FireStar.php.

Figure 1.

firestar sequence alignment outputs. (a) The PSI-BLAST alignment between the sequence of target T0312 and the best three structures. Information about binding sites is displayed alongside the alignment reliability scores. Per residue reliability scores returned by SQUARE are in blue and are based on residue similarity and conservation of neighbouring residues as described in Tress et al. (15). (b) MUSCLE multiple sequence alignment between the query and the sequence of all three PDB templates. Functionally important residues can be displayed dynamically.

Figure 2.

firestar structural alignments and visualization. (a) Users can select the region of the structure that they wish to align. (b) The structural alignment also shows information from functional residues and the reliability of the alignment according to SQUARE. (c) The Jmol visualization window. Buttons (not shown) permit the visualization of the superpositions of each separate functional site in the two structures.