In:
Algorithms for Molecular Biology, Springer Science and Business Media LLC, Vol. 3, No. 1 ( 2008-12)
Abstract:
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. It has a practical use in fast structural alignments and a potential use in finding those examples where sequence and structural similarities apparently disagree.
Type of Medium:
Online Resource
ISSN:
1748-7188
DOI:
10.1186/1748-7188-3-4
Language:
English
Publisher:
Springer Science and Business Media LLC
Publication Date:
2008
detail.hit.zdb_id:
2224970-9
SSG:
12
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