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Alignment algorithm for homology modeling and threading
Author(s) -
Alexandrov Nickolai N.,
Luethy Roland
Publication year - 1998
Publication title -
protein science
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.353
H-Index - 175
eISSN - 1469-896X
pISSN - 0961-8368
DOI - 10.1002/pro.5560070204
Subject(s) - threading (protein sequence) , structural alignment , alignment free sequence analysis , sequence alignment , homology modeling , computational biology , protein structure prediction , multiple sequence alignment , homology (biology) , structural bioinformatics , sequence (biology) , algorithm , loop modeling , computer science , protein structure , sequence homology , dna , peptide sequence , base sequence , biology , genetics , amino acid , gene , biochemistry , enzyme
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.