Comparative modeling without implicit sequence alignments.

Comparative modeling without implicit sequence alignments. Research Abstract Details 

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Comparative modeling without implicit sequence alignments. Abstract Text:

Andrzej Kolinski,Dominik Gront,

MOTIVATION: The number of known protein sequences is about thousand times larger than the number of experimentally solved 3D structures. For more than half of the protein sequences a close or distant structural analog could be identified. The key starting point in a classical comparative modeling is to generate the best possible sequence alignment with a template or templates. With decreasing sequence similarity, the number of errors in the alignments increases and these errors are the main causes of the decreasing accuracy of the molecular models generated. Here we propose a new approach to comparative modeling, which does not require the implicit alignment - the model building phase explores geometric, evolutionary and physical properties of a template (or templates). RESULTS: The proposed method requires prior identification of a template, although the initial sequence alignment is ignored. The model is built using a very efficient reduced representation search engine CABS to find the best possible superposition of the query protein onto the template represented as a 3D multi-featured scaffold. The criteria used include: sequence similarity, predicted secondary structure consistency, local geometric features and hydrophobicity profile. For more difficult cases, the new method qualitatively outperforms existing schemes of comparative modeling. The algorithm unifies de novo modeling, 3D threading and sequence-based methods. The main idea is general and could be easily combined with other efficient modeling tools as Rosetta, UNRES and others.

Comparative modeling without implicit sequence alignments. Publishing Authors By Initials

A Kolinski,D Gront,

For similar investigative techniques: genetic techniques: sequence analysis: sequence analysis, protein research abstracts see: investigative techniques: genetic techniques: sequence analysis: sequence analysis, protein research

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Comparative modeling without implicit sequence alignments. Journal Published:

PUBLICATION TYPE: Journal Article

Journal: Bioinformatics (Oxford, England)

VOLUME: 23

Page Numbers: 2522-7

Journal Abbreviation: Bioinformatics

ISSN: 1460-2059

DAY: 27

MONTH: 07

YEAR: 2007

Comparative modeling without implicit sequence alignments. Information

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LANGUAGE: eng

NlmUniqueID: 9808944

Comparative modeling without implicit sequence alignments. Keywords Mesh Terms:

KEYWORDS: Sequence Analysis, Protein

MESH TERMS: methods

Chemical & Substance for Abstract: Comparative modeling without implicit sequence alignments. Information

Substance Name: Proteins

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Grant and Affiliation Information for Comparative modeling without implicit sequence alignments.

AFFILIATION: University of Warsaw, Faculty of Chemistry, Pasteura 1 02-093 Warsaw, Poland.

Country: England

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MEDLINETA: Bioinformatics

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