tailieunhanh - 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 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 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 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 . 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.