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Motivation: Proteins are the main building blocks of life. They catalyze biological processes in living cells to sustain life and improve metabolism. They also act as biological scaffolds and are cell's workhorses. As a matter of fact, knowing their function is one of the most important milestones for understanding life.The function depends on the tertiary structure of the protein, but only for a fraction of amino acid sequences gathered in databases the structure is known. Thus, creation of efficient and accurate methods that predict function from sequences, based on already known function-sequence assignments, is a fundamental challenge in computational biology. Results: First, we show a detailed analysis of a usability of similarity search engines in the context of function prediction. Then we propose a simple and effective method for assigning function to sequences based on the results of similarity searches and information gathered from gene ontology annotation graphs. Availability: All data used for the analysis presented in this paper as well as raw result are available at the site: http://bio.cs.put.poznan.pl/funcpred/data/ Suplementary Material: Suplementary materials with additional charts are available at: http://bio.es.put.poznan.pl/funcpred/suplement/ Contact: protbio@cs.put.poznan.pl
Rocznik
Tom
Strony
173--191
Opis fizyczny
Bibliogr. 23 poz.
Twórcy
autor
autor
autor
autor
autor
- Institute of Computing Science, Poznan University of Technology, Poznan
Bibliografia
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- [2] D. Barthel, J. Hirst, J. Blazewicz, E. Burke, N. Krasnogor, Procksi: A decision support system for protein (structure) comparison, knowledge, similarity and information, BMC Bioinformatics 8 (416).
- [3] J. Blazewicz, P. Lukasiak, M. Milostan, Some operations research methods for analyzing protein sequences and structures, 4OR: A Quarterly Journal of Operations Research 4, no. 2 (2006) 91-123.
- [4] H. Berman, J. Westbrook, Z. Feng, G. Gilliland, T. Bhat, H. Weissig, I. Shindyalov, P. Bourne, The protein data bank, Nucleic Acids Research 28 (2000) 235-242.
- [5] W. Jaskowski, J. Blazewicz, P. Lukasiak, M. Milostan, N. Krasnogor, 3d-judge - a metaserver approach to protein structure prediction, Foundations of Computing and Decision Sciences 32 (1).
- [6] A. Kryshtafovych, A. Prlic, Z. Dmytriv, P. Daniluk, M. Milostan, V. Eyrich, T. Hubbard, K. Fidelis, New tools and expanded data analysis capabilities at the protein structure prediction center, Proteins 69 (S8) (2007) 19-26.
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Typ dokumentu
Bibliografia
Identyfikator YADDA
bwmeta1.element.baztech-article-BPP2-0014-0049