Protein sequence and structure alignments within one framework 英文参考文献.docVIP

Algorithms for Molecular Biology BioMedCentral Research Open Access Protein sequence and structure alignments within one framework Gundolf Schenk, Thomas Margraf and Andrew E Torda* Address: Centre for Bioinformatics, University of Hamburg, Bundesstr. 43, D-20146 Hamburg, Germany Email: Gundolf Schenk - schenk@zbh.uni-hamburg.de; Thomas Margraf - margraf@zbh.uni-hamburg.de; Andrew E Torda* - torda@zbh.uni- hamburg.de * Corresponding author Published: 1 April 2008 Received: 29 January 2008 Accepted: 1 April 2008 Algorithms for Molecular Biology 2008, 3:4 doi:10.1186/1748-7188-3-4 This article is available from: /content/3/1/4 ? 2008 Schenk et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: Protein structure alignments are usually based on very different techniques to sequence alignments. We propose a method which treats sequence, structure and even combined sequence + structure in a single framework. Using a probabilistic approach, we calculate a similarity measure which can be applied to fragments containing only protein sequence, structure or both simultaneously. Results: Proof-of-concept results are given for the different problems. For sequence alignments, the methodology is no better than conventional methods. For structure alignments, the techniques are very fast, reliable and tolerant of a range of alignment parameters. Combined sequence and structure alignments may provide a more reliable alignment for pairs of proteins where pure structural alignments can be misled by repetitive elements or apparent symmetries. Conclusion: The probabilistic framework has an elegance in principle, merging sequence and structure descriptors into a single framework. I