New tools and expanded data analysis capabilities at the Protein Structure Prediction Center

Abstract

We outline the main tasks performed by the Protein Structure Prediction Center in support of the CASP7 experiment and provide a brief review of the major measures used in the automatic evaluation of predictions. We describe in more detail the software developed to facilitate analysis of modeling success over and beyond the available templates and the adopted Java-based tool enabling visualization of multiple structural superpositions between target and several models/templates. We also give an overview of the CASP infrastructure provided by the Center and discuss the organization of the results web pages available through http://predictioncenter.org.

Figure 1

Schematic of the CASP7 prediction evaluation system. [Color figure can be viewed in the online issue, which is available at www.interscience.wiley.com.]

Figure 2

Information cell for target T0283. Clickable pictograms represent (1) tabulated numerical results, (2) 3D interactive representations of the target structures, (3) GDT plots, (4) alignment quality bar graphs, (5) comparison of models with template structures, and (6) SPICE-based interactive target/model/template visualization.

Figure 3

Strip charts displaying target–template-model proximity. Colors from blue to green show areas of potential model improvement over the template.

Figure 4

A screenshot of SPICE visualization server. The target/predictions/templates chosen in the middle panel are shown in the left-hand side structure display panel in a common frame of reference; the right-hand side panel displays the sequence of the currently active prediction and is interactively connected with the structure display panel: selecting sequence regions in the right-hand side panel highlights the corresponding regions in the protein structure.