CASP prediction center infrastructure and evaluation measures in CASP10 and CASP ROLL

Abstract

The Protein Structure Prediction Center at the University of California, Davis, supports the CASP experiments by identifying prediction targets, accepting predictions, performing standard evaluations, assisting independent CASP assessors, presenting and archiving results, and facilitating information exchange relating to CASP and structure prediction in general. We provide an overview of the CASP infrastructure implemented at the Center, and summarize standard measures used for evaluating predictions in the latest round of CASP. Several components were introduced or significantly redesigned for CASP10, in particular an improved assessors' common web-workspace; a Sphere Grinder visualization tool for analyzing local accuracy of predictions; brand new blocks for evaluation contact prediction and contact-assisted structure prediction; expanded evaluation and visualization tools for tertiary structure, refinement and quality assessment. Technical aspects of conducting the CASP10 and CASP ROLL experiments and relevant statistics are also provided.

Keywords: CASP; model evaluation; model visualization; protein structure modeling; protein structure prediction.

Figure 1

A comparison of the SphereGrinder 3D Profile views for two of the 502 models submitted on the CASP10 free modeling target T0693_D1. The SphereGrinder visualization allows a single glance perception of model quality, which for larger structures may become challenging, even when using structural representations. RMSD values (shown along the vertical z-axis) are color coded (1–15 A ° blue to red scale) and are plotted as a two-dimensional function of the position along the protein sequence (x axis) and of the sphere radius (y axis). Shift, rotation, and zoom in/out controls allow more detailed viewing. In this particular case, it can be seen that the first model (upper part of the figure) is of consistent quality along the chain, while the second is better in the first approximately one-fourth of the chain and considerably worse in the remaining sections. The sphere radii are calculated for values of 1–30 A ° and for 300 A ° (back plane of the profile).

Figure 2

Improvement of the contact-assisted models over the original ones for target Tc649. For every model, the color-coded bars show regions of improvement (blue-green) or decline (orange-red) over the original model submitted by the same group. Clicking on the strip graph opens a line plot (see callout) showing actual distances between the corresponding Cα atoms in the native structure and the assisted (blue line) and non-assisted (green line) models, and difference between them (red line).