As3p: A Fast Algorithm to Search Structurally Similar Proteins

Protein structure comparison is essential for understanding various aspects of protein structure, function and evolution. It can be used to explore the structural diversity and evolutionary patterns of protein families. In view of the above, a new algorithm is proposed which performs faster protein structure comparison using the peptide backbone torsional angles. It is fast, robust, computationally less expensive and efficient in finding structural similarities between two different protein structures and is also capable of identifying structural repeats within the same protein molecule.

[1]  R. Kolodny,et al.  Protein structure comparison: implications for the nature of 'fold space', and structure and function prediction. , 2006, Current opinion in structural biology.

[2]  K Henrick,et al.  Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions. , 2004, Acta crystallographica. Section D, Biological crystallography.

[3]  Liisa Holm,et al.  Searching protein structure databases with DaliLite v.3 , 2008, Bioinform..

[4]  Andrew E. Torda,et al.  The SALAMI protein structure search server , 2009, Nucleic Acids Res..

[5]  M. Murthy,et al.  Protein structural homology: a metric approach. , 2009, International journal of peptide and protein research.

[6]  Joël Pothier,et al.  Swelfe: a detector of internal repeats in sequences and structures , 2008, Bioinform..

[7]  Oliver Eulenstein,et al.  Bioinformatics Research and Applications , 2008 .

[8]  Gianluca Pollastri,et al.  Structural alphabets for protein structure classification: a comparison study. , 2009, Journal of molecular biology.

[9]  B. Rost,et al.  Protein structures sustain evolutionary drift. , 1997, Folding & design.

[10]  N Srinivasan,et al.  Comparison of sequence-based and structure-based phylogenetic trees of homologous proteins: Inferences on protein evolution , 2007, Journal of Biosciences.

[11]  Sean R Eddy,et al.  What is dynamic programming? , 2004, Nature Biotechnology.

[12]  Adam Godzik,et al.  Using an alignment of fragment strings for comparing protein structures , 2007, Bioinform..

[13]  A. Elofsson,et al.  Structure is three to ten times more conserved than sequence—A study of structural response in protein cores , 2009, Proteins.

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

[15]  Guoli Wang,et al.  PISCES: a protein sequence culling server , 2003, Bioinform..

[16]  Krishna Sekar,et al.  ProSTRIP: A method to find similar structural repeats in three-dimensional protein structures , 2010, Comput. Biol. Chem..

[17]  Wei-Mou Zheng.  The Use of a Conformational Alphabet for Fast Alignment of Protein Structures , 2008, ISBRA.

[18]  A. Giuliani,et al.  A computational approach identifies two regions of Hepatitis C Virus E1 protein as interacting domains involved in viral fusion process , 2009, BMC Structural Biology.