Measuring the similarity of protein structures by means of the universal similarity metric. Export

@article{citeulike:165613, abstract = {MOTIVATION: As an increasing number of protein structures become available, the need for algorithms that can quantify the similarity between protein structures increases as well. Thus, the comparison of proteins' structures, and their clustering accordingly to a given similarity measure, is at the core of today's biomedical research. In this paper, we show how an algorithmic information theory inspired Universal Similarity Metric (USM) can be used to calculate similarities between protein pairs. The method, besides being theoretically supported, is surprisingly simple to implement and computationally efficient. RESULTS: Structural similarity between proteins in four different datasets was measured using the USM. The sample employed represented alpha, beta, alpha-beta, tim-barrel, globins and serpine protein types. The use of the proposed metric allows for a correct measurement of similarity and classification of the proteins in the four datasets. AVAILABILITY: All the scripts and programs used for the preparation of this paper are available at http://www.cs.nott.ac.uk/\~{}nxk/USM/protocol.html. In that web-page the reader will find a brief description on how to use the various scripts and programs.}, address = {Automated Scheduling, Optimisation and Planning Group, University of Nottingham, Nottingham NG8 1BB, UK. Natalio.Krasnogor@nottingham.ac.uk}, author = {Krasnogor, N. and Pelta, D. A.}, citeulike-article-id = {165613}, citeulike-linkout-0 = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/20/7/1015}, citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/14751983}, citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=14751983}, day = {1}, issn = {1367-4803}, journal = {Bioinformatics}, keywords = {protein, similarity, structure}, month = {May}, number = {7}, pages = {1015--1021}, posted-at = {2005-11-29 18:54:04}, priority = {2}, title = {Measuring the similarity of protein structures by means of the universal similarity metric.}, url = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/20/7/1015}, volume = {20}, year = {2004} }

TY - JOUR ID - citeulike:165613 L3 - citeulike-article-id:165613 N2 - MOTIVATION: As an increasing number of protein structures become available, the need for algorithms that can quantify the similarity between protein structures increases as well. Thus, the comparison of proteins' structures, and their clustering accordingly to a given similarity measure, is at the core of today's biomedical research. In this paper, we show how an algorithmic information theory inspired Universal Similarity Metric (USM) can be used to calculate similarities between protein pairs. The method, besides being theoretically supported, is surprisingly simple to implement and computationally efficient. RESULTS: Structural similarity between proteins in four different datasets was measured using the USM. The sample employed represented alpha, beta, alpha-beta, tim-barrel, globins and serpine protein types. The use of the proposed metric allows for a correct measurement of similarity and classification of the proteins in the four datasets. AVAILABILITY: All the scripts and programs used for the preparation of this paper are available at http://www.cs.nott.ac.uk/~nxk/USM/protocol.html. In that web-page the reader will find a brief description on how to use the various scripts and programs. IS - 7 JF - Bioinformatics SN - 1367-4803 AD - Automated Scheduling, Optimisation and Planning Group, University of Nottingham, Nottingham NG8 1BB, UK. Natalio.Krasnogor@nottingham.ac.uk EP - 1021 TI - Measuring the similarity of protein structures by means of the universal similarity metric. VL - 20 SP - 1015 KW - protein KW - similarity KW - structure AU - Krasnogor, N AU - Pelta, DA PY - 2004/05/01/ UR - http://bioinformatics.oxfordjournals.org/cgi/content/abstract/20/7/1015 ER -