SABERTOOTH: protein structural alignment based on a vectorial structure representation-2

<p><b>Copyright information:</b></p><p>Taken from "SABERTOOTH: protein structural alignment based on a vectorial structure representation"</p><p>http://www.biomedcentral.com/1471-2105/8/425</p><p>BMC Bioinformatics 2007;8():425-425.</p><p>Published online 31 Oct 2007</p><p>PMCID:PMC2257979.</p><p></p>ms over the test set, the PSI (i.e. including short aligned fragments) are shown as shadows. The influence of short fragments is most dramatic for TM-align and SHEBA, as expected from Fig. 7. In the right column, differences to the results of SABERTOOTH are shown for direct comparison. Positive values connote higher rPSI for SABERTOOTH. Mean values may be found in Table 2

SABERTOOTH: protein structural alignment based on a vectorial structure representation-1

<p><b>Copyright information:</b></p><p>Taken from "SABERTOOTH: protein structural alignment based on a vectorial structure representation"</p><p>http://www.biomedcentral.com/1471-2105/8/425</p><p>BMC Bioinformatics 2007;8():425-425.</p><p>Published online 31 Oct 2007</p><p>PMCID:PMC2257979.</p><p></p>the algorithms assessed here. The behaviour found is very different for the different schemes. The total number of residues in fragments of sizes smaller than four sums up to 1.01% for SABERTOOTH, 0.13% for MAMMOTH, 1.18% for MAMMTOH-mult, 0.33% for DaliLite, 7.25% for TM-align, 2.22% for CE, and to 12.20% for SHEBA. Those aligned pairs are most likely not significant and should be omitted when the PSI is computed

SABERTOOTH: protein structural alignment based on a vectorial structure representation-0

<p><b>Copyright information:</b></p><p>Taken from "SABERTOOTH: protein structural alignment based on a vectorial structure representation"</p><p>http://www.biomedcentral.com/1471-2105/8/425</p><p>BMC Bioinformatics 2007;8():425-425.</p><p>Published online 31 Oct 2007</p><p>PMCID:PMC2257979.</p><p></p>l rotation. Aligned regions that are closer in space than 4 Å are marked in green, aligned regions further apart are marked in yellow, and regions that are opposite to gaps in the alignment are marked in light blue and light red

Empirical energy functions evaluated for each models and for the corresponding region of the template show that the predicted stability decrease is moderate.

<p>Empirical energy functions evaluated for each models and for the corresponding region of the template show that the predicted stability decrease is moderate.</p

Protein-protein interaction networks for interactions experimentally observed for human centrosomal proteins.

<p>The color code represents betweeness centrality, a graph theoretic measure of the centrality of a node in a network, red representing the most central node.</p

Number of occurrences of domains predicted by SMART.

<p>Only domains with more than 3 occurrences are shown.</p

Fraction of protein length that is predicted to be disordered, coiled-coil, or modeled by homology.

<p>The plots represent the distribution of the percentage of protein length that has been (A) predicted to be disordered and coiled-coil at the same time; (B) Predicted to be disordered and not coiled-coil; (C) modeled; (D) Predicted to have regular secondary structure and not to be disordered neither coiled-coil, but not modeled.</p

Number of residues and number of models for each protein.

<p>The plots represent the distribution of the number of residues of the longest isoform of centrosomal genes (A) and the number of structural models obtained for each protein (B).</p