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Protein Science, Vol 7, Issue 2 254-258, Copyright © 1998 by Cold Spring Harbor Laboratory Press

ARTICLE

Alignment algorithm for homology modeling and threading

N. A. ALEXANDROV and R. LUETHY
Amgen, Inc., 1840 DeHavilland Drive, Thousand Oaks, California 91320-1789

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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