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A profile-based protein sequence alignment algorithm for a domain clustering database

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3 Author(s)
Lin Xu ; Inst. of Comput. Technol.,, Chinese Acad. of Sci. ; Fa Zhang ; Zhiyong Liu

Aiming at the two main shortcomings in Homology Modeling, we have designed and established a domain clustering database. Searching the database is a fundamental work for it. However, current alignment algorithms are mainly based on the sequences, ignoring the structure conservation in domain. This paper proposed a profile-based alignment which considers the structure information into the profile, based on the character of our domain database. We designed an experiment within the database. The results show that both the quality and sensitivity of our scheme are better than pure Smith-Waterman and sequence-based profile algorithms. We strongly believe that this work can help to improve the protein structure prediction

Published in:

Computational Intelligence and Bioinformatics and Computational Biology, 2006. CIBCB '06. 2006 IEEE Symposium on

Date of Conference:

28-29 Sept. 2006