Comparison of protein structures by growing neighborhood alignments

Background: Design of protein structure comparison algorithm is an important research issue, having far reaching implications. In this article, we describe a protein structure comparison scheme, which is capable of detecting correct alignments even in difficult cases, e.g. non-topological similarities. The proposed method computes protein structure alignments by comparing, small substructures, called neighborhoods. Two different types of neighborhoods, sequence and structure, are defined, and two algorithms arising out of the scheme are detailed. A new method for computing equivalences having non-topological similarities from pairwise similarity score is described. A novel and fast technique for comparing sequence neighborhoods is also developed. Results: The experimental results show that the current programs show better performance on Fischer and Novotny's benchmark datasets, than state of the art programs, e.g. DALI, CE and SSM. Our programs were also found to calculate correc...

• Type: Journal
• Year: 2007
• Where: BMCBI
• Authors: Sourangshu Bhattacharya, Chiranjib Bhattacharyya, Nagasuma Chandra
• Keywords: BMCBI 2007, Correct Alignments, Protein Structure Comparison, Protein Structures