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Evaluation of protein fold comparison servers.
Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Cell and Molecular Biology. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Cell and Molecular Biology, Structural Molecular Biology.
Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Cell and Molecular Biology. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Cell and Molecular Biology, Structural Molecular Biology. ICM. (Strukturbiologi)
2004 (English)In: Proteins, ISSN 1097-0134, Vol. 54, no 2, 260-70 p.Article in journal (Refereed) Published
Abstract [en]

When a new protein structure has been determined, comparison with the database of known structures enables classification of its fold as new or belonging to a known class of proteins. This in turn may provide clues about the function of the protein. A large number of fold comparison programs have been developed, but they have never been subjected to a comprehensive and critical comparative analysis. Here we describe an evaluation of 11 publicly available, Web-based servers for automatic fold comparison. Both their functionality (e.g., user interface, presentation, and annotation of results) and their performance (i.e., how well established structural similarities are recognized) were assessed. The servers were subjected to a battery of performance tests covering a broad spectrum of folds as well as special cases, such as multidomain proteins, Calpha-only models, new folds, and NMR-based models. The CATH structural classification system was used as a reference. These tests revealed the strong and weak sides of each server. On the whole, CE, DALI, MATRAS, and VAST showed the best performance, but none of the servers achieved a 100% success rate. Where no structurally similar proteins are found by any individual server, it is recommended to try one or two other servers before any conclusions concerning the novelty of a fold are put on paper.

Place, publisher, year, edition, pages
2004. Vol. 54, no 2, 260-70 p.
Keyword [en]
Comparative Study, Computational Biology, Cyclophilins/chemistry/classification/metabolism, Databases; Protein, Information Storage and Retrieval, Internet, Protein Folding, Protein Structure; Tertiary, Proteins/*chemistry/*classification/metabolism, Research Support; Non-U.S. Gov't, Software, Structure-Activity Relationship, User-Computer Interface
Identifiers
URN: urn:nbn:se:uu:diva-71941PubMedID: 14696188OAI: oai:DiVA.org:uu-71941DiVA: diva2:99852
Available from: 2006-12-15 Created: 2006-12-15 Last updated: 2011-01-12

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Novotny, Marian

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