Tuyển tập các báo cáo nghiên cứu về y học được đăng trên tạp chí y học Minireview cung cấp cho các bạn kiến thức về ngành y đề tài: Kappa-alpha plot derived structural alphabet and BLOSUM-like substitution matrix for rapid search of protein structure database. | Method Open Access Kappa-alpha plot derived structural alphabet and BLOSUM-like substitution matrix for rapid search of protein structure database Chi-Hua TungH Jhang-Wei Huang and Jinn-Moon YangH n Addresses institute of Bioinformatics National Chiao Tung University 75 Po-Ai Street Hsinchu 30050 Taiwan. Department of Biological Science and Technology National Chiao Tung University 75 Po-Ai Street Hsinchu 30050 Taiwan. Core Facility for Structural Bioinformatics National Chiao Tung University 75 Po-Ai Street Hsinchu Taiwan. H These authors contributed equally to this work. Correspondence Jinn-Moon Yang. Email moon@ Published 3 March 2007 Received 21 November 2006 Genome Biology 2007 8 R3 I doi gb-2007-8-3-r3l R .d. J5 ianuiry 2007 gy g Accepted 3 March 2007 The electronic version of this article is the complete one and can be found online at http 2007 8 3 R3I 2007 Tung et al. licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License http licenses by which permits unrestricted use distribution and reproduction in any medium provided the original work is properly cited. Abstract We present a novel protein structure database search tool 3D-BLAST that is useful for analyzing novel structures and can return a ranked list of alignments. This tool has the features of BLAST for example robust statistical basis and effective and reliable search capabilities and employs a kappaalpha K a plot derived structural alphabet and a new substitution matrix. 3D-BLAST searches more than 12 000 protein structures in s and yields good results in zones with low sequence similarity. Background A major challenge facing structural biology research in the postgenomics era is to discover the biologic functions of genes identified by large-scale sequencing efforts. As protein structures increasingly become available and structural genomics research
