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Appears in Collections:Computing Science and Mathematics Journal Articles
Peer Review Status: Refereed
Title: ProCKSI: A decision support system for Protein (Structure) Comparison, Knowledge, Similarity and Information
Authors: Barthel, Daniel
Hirst, Jonathan D
Blazewicz, Jacek
Burke, Edmund
Krasnogor, Natalio
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Issue Date: Oct-2007
Publisher: BioMed Central Ltd
Citation: Barthel D, Hirst JD, Blazewicz J, Burke E & Krasnogor N (2007) ProCKSI: A decision support system for Protein (Structure) Comparison, Knowledge, Similarity and Information, BMC Bioinformatics, 8, Art. No.: 416.
Abstract: Background: We introduce the decision support system for Protein (Structure) Comparison, Knowledge, Similarity and Information (ProCKSI). ProCKSI integrates various protein similarity measures through an easy to use interface that allows the comparison of multiple proteins simultaneously. It employs the Universal Similarity Metric (USM), the Maximum Contact Map Overlap (MaxCMO) of protein structures and other external methods such as the DaliLite and the TM-align methods, the Combinatorial Extension (CE) of the optimal path, and the FAST Align and Search Tool (FAST). Additionally, ProCKSI allows the user to upload a user-defined similarity matrix supplementing the methods mentioned, and computes a similarity consensus in order to provide a rich, integrated, multicriteria view of large datasets of protein structures. Results: We present ProCKSI's architecture and workflow describing its intuitive user interface, and show its potential on three distinct test-cases. In the first case, ProCKSI is used to evaluate the results of a previous CASP competition, assessing the similarity of proposed models for given targets where the structures could have a large deviation from one another. To perform this type of comparison reliably, we introduce a new consensus method. The second study deals with the verification of a classification scheme for protein kinases, originally derived by sequence comparison by Hanks and Hunter, but here we use a consensus similarity measure based on structures. In the third experiment using the Rost and Sander dataset (RS126), we investigate how a combination of different sets of similarity measures influences the quality and performance of ProCKSI's new consensus measure. ProCKSI performs well with all three datasets, showing its potential for complex, simultaneous multi-method assessment of structural similarity in large protein datasets. Furthermore, combining different similarity measures is usually more robust than relying on one single, unique measure. Conclusion: Based on a diverse set of similarity measures, ProCKSI computes a consensus similarity profile for the entire protein set. All results can be clustered, visualised, analysed and easily compared with each other through a simple and intuitive interface.
Type: Journal Article
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Rights: © 2007 Barthel et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Affiliation: University of Nottingham
University of Nottingham
Poznan University of Technology
Deputy Principal's Office
University of Nottingham

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