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Báo cáo sinh học: "An automated stochastic approach to the identification of the protein specificity determinants and functional subfamilies"

Tuyển tập các báo cáo nghiên cứu về sinh học được đăng trên tạp chí y học Molecular Biology cung cấp cho các bạn kiến thức về ngành sinh học đề tài: An automated stochastic approach to the identification of the protein specificity determinants and functional subfamilies. | Mazin et al. Algorithms for Molecular Biology 2010 5 29 http www.almob.Org content 5 1 29 AMR ALGORITHMS FOR MOLECULAR BIOLOGY RESEARCH Open Access An automated stochastic approach to the identification of the protein specificity determinants and functional subfamilies 1 1.3 1.3 1.3 3 Pavel V Mazin Mikhail S Gelfand Andrey A Mironov Aleksandra B Rakhmaninova Anatoly R Rubinov Robert B Russell 2 Olga V Kalinina2 3 Abstract Background Recent progress in sequencing and 3 D structure determination techniques stimulated development of approaches aimed at more precise annotation of proteins that is prediction of exact specificity to a ligand or more broadly to a binding partner of any kind. Results We present a method SDPclust for identification of protein functional subfamilies coupled with prediction of specificity-determining positions SDPs . SDPclust predicts specificity in a phylogeny-independent stochastic manner which allows for the correct identification of the specificity for proteins that are separated on a phylogenetic tree but still bind the same ligand. SDPclust is implemented as a Web-server http bioinf.fbb.msu.ru SDPfoxWeb and a stand-alone Java application available from the website. Conclusions SDPclust performs a simultaneous identification of specificity determinants and specificity groups in a statistically robust and phylogeny-independent manner. Background The current explosion of data on protein sequences and structures lead to the emergence of techniques that go beyond standard annotation approaches i.e. annotation by close homolog and homology-based family identification. These approaches usually start with a set of related sequences and perform a detailed analysis of each alignment position 1-15 . One of problems that such analysis can tackle is analysis of protein specificity. Let us assume that a protein family has undergone an ancient duplication that resulted in proteins that are related but perform different functions in the same organism.