期刊论文详细信息
BMC Bioinformatics
ConEVA: a toolbox for comprehensive assessment of protein contacts
Software
Jie Hou1  Badri Adhikari1  Jackson Nowotny1  Debswapna Bhattacharya1  Jianlin Cheng2 
[1] Department of Computer Science, University of Missouri, 65211, Columbia, MO, USA;Department of Computer Science, University of Missouri, 65211, Columbia, MO, USA;Informatics Institute, University of Missouri, 65211, Columbia, MO, USA;C. Bond Life Science Center, University of Missouri, 65211, Columbia, MO, USA;
关键词: Protein contact assessment;    Chord diagrams;    Contact maps;    Contact visualization;    Jaccard similarity;   
DOI  :  10.1186/s12859-016-1404-z
 received in 2016-07-01, accepted in 2016-12-01,  发布年份 2016
来源: Springer
PDF
【 摘 要 】

BackgroundIn recent years, successful contact prediction methods and contact-guided ab initio protein structure prediction methods have highlighted the importance of incorporating contact information into protein structure prediction methods. It is also observed that for almost all globular proteins, the quality of contact prediction dictates the accuracy of structure prediction. Hence, like many existing evaluation measures for evaluating 3D protein models, various measures are currently used to evaluate predicted contacts, with the most popular ones being precision, coverage and distance distribution score (Xd).ResultsWe have built a web application and a downloadable tool, ConEVA, for comprehensive assessment and detailed comparison of predicted contacts. Besides implementing existing measures for contact evaluation we have implemented new and useful methods of contact visualization using chord diagrams and comparison using Jaccard similarity computations. For a set (or sets) of predicted contacts, the web application runs even when a native structure is not available, visualizing the contact coverage and similarity between predicted contacts. We applied the tool on various contact prediction data sets and present our findings and insights we obtained from the evaluation of effective contact assessments. ConEVA is publicly available at http://cactus.rnet.missouri.edu/coneva/.ConclusionConEVA is useful for a range of contact related analysis and evaluations including predicted contact comparison, investigation of individual protein folding using predicted contacts, and analysis of contacts in a structure of interest.

【 授权许可】

CC BY   
© The Author(s). 2016

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