Alignment algorithm for homology modeling and threading.

N N Alexandrov; R Luethy

doi:10.1002/pro.5560070204

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Alignment algorithm for homology modeling and threading.

N N Alexandrov·R Luethy

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Abstract

A DNA/protein sequence comparison is a popular computational tool for molecular biologists. Finding a good alignment implies an evolutionary and/or functional relationship between proteins or genomic loci. Sequential similarity between two proteins indicates their structural resemblance, providing a practical approach for structural modeling, when structure of one of these proteins is known. The first step in the homology modeling is a construction of an accurate sequence alignment. The commonly used alignment algorithms do not provide an adequate treatment of the structurally mismatched residues in locally dissimilar regions. We propose a simple modification of the existing alignment algorithm which treats these regions properly and demonstrate how this modification improves sequence alignments in real proteins.

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Algorithms Amino Acid Sequence Animals Helix-Loop-Helix Motifs Models, Molecular Molecular Sequence Data Sequence Homology, Amino Acid Journal Article

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BibTeX RIS

N N Alexandrov, R Luethy. 1998. Alignment algorithm for homology modeling and threading.. https://doi.org/10.1002/pro.5560070204

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