Protein sequence and structure alignments within one framework.

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

SUBMITTER: Schenk G 

PROVIDER: S-EPMC2390564 | biostudies-literature | 2008 Apr

REPOSITORIES: biostudies-literature