Local alignment refinement using structural assessment.

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Serval ID
serval:BIB_FB638F1C1F58
Type
Article: article from journal or magazin.
Collection
Publications
Institution
Title
Local alignment refinement using structural assessment.
Journal
PLoS ONE
Author(s)
Chodanowski P., Grosdidier A., Feytmans E., Michielin O.
ISSN
1932-6203
Publication state
Published
Issued date
2008
Peer-reviewed
Oui
Volume
3
Number
7
Pages
e2645
Language
english
Notes
Publication types: Journal Article ; Research Support, Non-U.S. Gov't
Abstract
Homology modeling is the most commonly used technique to build a three-dimensional model for a protein sequence. It heavily relies on the quality of the sequence alignment between the protein to model and related proteins with a known three dimensional structure. Alignment quality can be assessed according to the physico-chemical properties of the three dimensional models it produces.In this work, we introduce fifteen predictors designed to evaluate the properties of the models obtained for various alignments. They consist of an energy value obtained from different force fields (CHARMM, ProsaII or ANOLEA) computed on residue selected around misaligned regions. These predictors were evaluated on ten challenging test cases. For each target, all possible ungapped alignments are generated and their corresponding models are computed and evaluated.The best predictor, retrieving the structural alignment for 9 out of 10 test cases, is based on the ANOLEA atomistic mean force potential and takes into account residues around misaligned secondary structure elements. The performance of the other predictors is significantly lower. This work shows that substantial improvement in local alignments can be obtained by careful assessment of the local structure of the resulting models.
Keywords
Algorithms, Amino Acid Sequence, Animals, Humans, Molecular Sequence Data, Proteins, Sequence Alignment, Structural Homology, Protein
Pubmed
Web of science
Open Access
Yes
Create date
11/03/2009 13:49
Last modification date
20/08/2019 16:26
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