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

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

[1]  A G Murzin,et al.  SCOP: a structural classification of proteins database for the investigation of sequences and structures. , 1995, Journal of molecular biology.

[2]  J. Thompson,et al.  CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. , 1994, Nucleic acids research.

[3]  Thomas L. Madden,et al.  Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. , 1997, Nucleic acids research.

[4]  W. Pearson.  Rapid and sensitive sequence comparison with FASTP and FASTA. , 1990, Methods in enzymology.

[5]  Rolf Apweiler,et al.  InterProScan - an integration platform for the signature-recognition methods in InterPro , 2001, Bioinform..

[6]  T. N. Bhat,et al.  The Protein Data Bank , 2000, Nucleic Acids Res..

[7]  P E Bourne,et al.  Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. , 1998, Protein engineering.

[8]  Michael Brudno,et al.  Fast and sensitive multiple alignment of large genomic sequences , 2003, BMC Bioinformatics.

[9]  Cathy H. Wu,et al.  InterPro, progress and status in 2005 , 2004, Nucleic Acids Res..

[10]  Sean R. Eddy,et al.  Profile hidden Markov models , 1998, Bioinform..

[11]  Zhiyong Liu,et al.  The Construction of Structural Templates for the Modeling of conserved protein Domains , 2005, Advances in Bioinformatics and Its Applications.

[12]  D. Higgins,et al.  T-Coffee: A novel method for fast and accurate multiple sequence alignment. , 2000, Journal of molecular biology.

[13]  Owen White,et al.  The TIGRFAMs database of protein families , 2003, Nucleic Acids Res..

[14]  Christus,et al.  A General Method Applicable to the Search for Similarities in the Amino Acid Sequence of Two Proteins , 2022 .

[15]  M S Waterman,et al.  Identification of common molecular subsequences. , 1981, Journal of molecular biology.

[16]  A. D. McLachlan,et al.  Profile analysis: detection of distantly related proteins. , 1987, Proceedings of the National Academy of Sciences of the United States of America.

[17]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.

[18]  Peer Bork,et al.  SMART 4.0: towards genomic data integration , 2004, Nucleic Acids Res..

[19]  C. Sander,et al.  Protein structure comparison by alignment of distance matrices. , 1993, Journal of molecular biology.