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

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

Andriy Kryshtafovych et al. Proteins. 2007.

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.

(c) 2007 Wiley-Liss, Inc.

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Figures

Figure 1
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
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
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
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.

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References

    1. Kryshtafovych A, Milostan M, Szajkowski L, Daniluk P, Fidelis K. CASP6 data processing and automatic evaluation at the protein structure prediction center. Proteins. 2005;61(Suppl 7):19–23. - PubMed
    1. Eyrich VA, Kryshtafovych A, Milostan M, Fidelis K. System for accepting server predictions in CASP6. Proteins. 2005;61(Suppl 7):24–26. - PubMed
    1. Zemla A. LGA: a method for finding 3D similarities in protein structures. Nucleic Acids Res. 2003;31:3370–3374. - PMC - PubMed
    1. Hvidsten TR, Kryshtafovych A, Komorowski J, Fidelis K. A novel approach to fold recognition using sequence-derived properties from sets of structurally similar local fragments of proteins. Bioinformatics. 2003;19(Suppl 2):II81–II91. - PubMed
    1. Ortiz AR, Strauss CE, Olmea O. MAMMOTH matching molecular models obtained from theory: an automated method for model comparison. Protein Sci. 2002;11:2606–2621. - PMC - PubMed

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