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- Title
Fast and accurate methods for predicting short-range constraints in protein models.
- Authors
Gront, Dominik; Kolinski, Andrzej
- Abstract
Protein modeling tools utilize many kinds of structural information that may be predicted from amino acid sequence of a target protein or obtained from experiments. Such data provide geometrical constraints in a modeling process. The main aim is to generate the best possible consensus structure. The quality of models strictly depends on the imposed conditions. In this work we present an algorithm, which predicts short-range distances between Cα atoms as well as a set of short structural fragments that possibly share structural similarity with a query sequence. The only input of the method is a query sequence profile. The algorithm searches for short protein fragments with high sequence similarity. As a result a statistics of distances observed in the similar fragments is returned. The method can be used also as a scoring function or a short-range knowledge-based potential based on the computed statistics.
- Subjects
PROTEIN analysis; AMINO acid analysis; AMINO acid sequence; QUERY (Information retrieval system); ALGORITHMS
- Publication
Journal of Computer-Aided Molecular Design, 2008, Vol 22, Issue 11, p783
- ISSN
0920-654X
- Publication type
Article
- DOI
10.1007/s10822-008-9213-8