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Analysis of CASP8 targets, predictions and assessment methods.

ABSTRACT: Results of the recent Critical Assessment of Techniques for Protein Structure Prediction, CASP8, present several valuable sources of information. First, CASP targets comprise a realistic sample of currently solved protein structures and exemplify the corresponding challenges for predictors. Second, the plethora of predictions by all possible methods provides an unusually rich material for evolutionary analysis of target proteins. Third, CASP results show the current state of the field and highlight specific problems in both predicting and assessing. Finally, these data can serve as grounds to develop and analyze methods for assessing prediction quality. Here we present results of our analysis in these areas. Our objective is not to duplicate CASP assessment, but to use our unique experience as former CASP5 assessors and CASP8 predictors to (i) offer more insights into CASP targets and predictions based on expert analysis, including invaluable analysis prior to target structure release; and (ii) develop an assessment methodology tailored towards current challenges in the field. Specifically, we discuss preparing target structures for assessment, parsing protein domains, balancing evaluations based on domains and on whole chains, dividing targets into categories and developing new evaluation scores. We also present evolutionary analysis of the most interesting and challenging targets.Database URL: Our results are available as a comprehensive database of targets and predictions at http://prodata.swmed.edu/CASP8.

SUBMITTER: Shi S

PROVIDER: S-EPMC2794793 | biostudies-literature | 2009

REPOSITORIES: biostudies-literature

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Analysis of CASP8 targets, predictions and assessment methods.

Shi Shuoyong S Pei Jimin J Sadreyev Ruslan I RI Kinch Lisa N LN Majumdar Indraneel I Tong Jing J Cheng Hua H Kim Bong-Hyun BH Grishin Nick V NV

Database : the journal of biological databases and curation 20090414

Results of the recent Critical Assessment of Techniques for Protein Structure Prediction, CASP8, present several valuable sources of information. First, CASP targets comprise a realistic sample of currently solved protein structures and exemplify the corresponding challenges for predictors. Second, the plethora of predictions by all possible methods provides an unusually rich material for evolutionary analysis of target proteins. Third, CASP results show the current state of the field and highli ...[more]

PMID: 20157476

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Project description:BackgroundPatients with a mental illness are more likely to develop, and die from, cardiovascular diseases (CVD), necessitating optimal CVD-risk (CVR)-assessment to enable early detection and treatment. Whereas psychiatrists use the metabolic syndrome (MetS)-concept to estimate CVR, GPs use absolute risk-models. Additionally, two PRIMROSE-models have been specifically designed for patients with severe mental illness. We aimed to assess the agreement in risk-outcomes between these CVR-methods.MethodsTo compare risk-outcomes across the various CVR-methods, we used somatic information of psychiatric outpatients from the PHAMOUS-, and MOPHAR-database, aged 40-70 years, free of past or current CVD and diabetes. We investigated: (1) the degree-of-agreement between categorical assessments (i.e. MetS-status vs. binary risk-categories); (2) non-parametric correlations between the number of MetS-criteria and absolute risks; and (3) strength-of-agreement between absolute risks.ResultsSeven thousand twenty-nine measurements of 3509 PHAMOUS-patients, and 748 measurements of 748 MOPHAR-patients, were included. There was systematic disagreement between the categorical CVR-assessments (all p < 0.036). Only MetS-status versus binary Framingham-assessment had a fair strength-of-agreement (κ = 0.23-0.28). The number of MetS-criteria and Framingham-scores, as well as MetS-criteria and PRIMROSE lipid-scores, showed a moderate-strong correlation (τ = 0.25-0.34). Finally, only the continuous PRIMROSE desk and lipid-outcomes showed moderate strength-of-agreement (ρ = 0.91).ConclusionsThe varying methods for CVR-assessment yield unequal risk predictions, and, consequently, carry the risk of significant disparities regarding treatment initiation in psychiatric patients. Considering the significantly increased health-risks in psychiatric patients, CVR-models should be recalibrated to the psychiatric population from adolescence onwards, and uniformly implemented by health care providers.Trial registrationThe MOPHAR research has been prospectively registered with the Netherlands Trial Register on 19th of November 2014 (NL4779).

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Analysis of CASP8 targets, predictions and assessment methods.

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Analysis of CASP8 targets, predictions and assessment methods.

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