Alexandrov N N, Luethy R
Amgen, Inc., Thousand Oaks, California 91320-1789, USA.
Protein Sci. 1998 Feb;7(2):254-8. doi: 10.1002/pro.5560070204.
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.
DNA/蛋白质序列比对是分子生物学家常用的一种计算工具。找到一个良好的比对意味着蛋白质或基因组位点之间存在进化和/或功能关系。两种蛋白质之间的序列相似性表明它们的结构相似性，当其中一种蛋白质的结构已知时，这为结构建模提供了一种实用方法。同源建模的第一步是构建精确的序列比对。常用的比对算法不能充分处理局部不同区域中结构不匹配的残基。我们提出了对现有比对算法的一种简单修改，该修改能正确处理这些区域，并展示了这种修改如何改善真实蛋白质中的序列比对。
