ALIGNMENT-BASED EXTENSION TO DDPIN FEATURE EXTRACTION

Finding similarity between a pair of protein structures is one of the fundamental tasks in many areas of bioinformatical research such as protein structure prediction, function mapping, etc. We propose a method for finding pairing of amino acids based on densities of the structures and we also propose a modification to the original template modeling-score (TM-Score) rotation algorithm that assess similarity score to this alignment. Proposed modification is faster than TM and comparably robust according to non-optimal parts in the alignment. We measure the qualities of the algorithm in terms of structural classification of proteins (SCOP) classification accuracy. Regarding the accuracy, our solution outperforms the contemporary solutions at two out of three tested levels of the SCOP hierarchy.

[1]  S. B. Needleman,et al.  A general method applicable to the search for similarities in the amino acid sequence of two proteins. , 1970, Journal of molecular biology.

[2]  David Hoksza,et al.  On the Effectiveness of Distances Measuring Protein Structure Similarity , 2009, 2009 Second International Workshop on Similarity Search and Applications.

[3]  Yang Zhang,et al.  Scoring function for automated assessment of protein structure template quality , 2004, Proteins.

[4]  R. Lathrop.  The protein threading problem with sequence amino acid interaction preferences is NP-complete. , 1994, Protein engineering.

[5]  W. Kabsch.  A solution for the best rotation to relate two sets of vectors , 1976 .

[6]  Ralf Zimmer,et al.  Protein structure alignment considering phenotypic plasticity , 2008, ECCB.

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

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

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

[10]  J. Skolnick,et al.  TM-align: a protein structure alignment algorithm based on the TM-score , 2005, Nucleic acids research.

[11]  Patrice Koehl,et al.  The ASTRAL Compendium in 2004 , 2003, Nucleic Acids Res..

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

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

[14]  W R Taylor,et al.  A holistic approach to protein structure alignment. , 1989, Protein engineering.

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

[16]  K Schulten,et al.  VMD: visual molecular dynamics. , 1996, Journal of molecular graphics.

[17]  David Hoksza.  DDPIn - Distance and density based protein indexing , 2009, 2009 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology.

[18]  Ralf Zimmer,et al.  Vorolign - fast structural alignment using Voronoi contacts , 2007, Bioinform..

[19]  Ismail Hakki Toroslu,et al.  Integrated search and alignment of protein structures , 2008, Bioinform..