Abstract
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.
Keywords
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Berman, H.M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T.N., Weissig, H., Shindyalov, I.N., Bourne, P.E.: The Protein Data Bank. Nucleic Acids Res. 28, 235–242 (2000)
Zotenko, E., Gogan, R.I., Wilbur, W.J., O’Leary, D.P., Przytycka, T.M.: Structural Footprinting In Protein Structure Comparison: the Impact of Structural Fragments. BMC Struct. Biol. 7, 53–66 (2007)
Rost, B.: Protein Structures Sustain Evolutionary Drift. Fold Des. 24, S19–S24 (1997)
Balaji, S., Srinivasan, N.: Comparison of Sequence-Based and Structure-Based Phylogenetic Trees of Homologous Proteins: Inferences on Protein Evolution. J. Biosci. 32, 83–96 (2007)
Illergard, K., Ardell, D.H., Elofsson, A.: Structure is Three To Ten Times More Conserved Than Sequence–A Study Of Structural Response In Protein Cores. Protein 77, 499–508 (2009)
Le, Q., Pollastri, G., Koehl, P.: Structural Alphabets for Protein Structure Classification: A Comparison Study. J. Mol. Biol. 387, 431–450 (2009)
Kolodny, R., Petrey, D., Honig, B.: Protein Structure Comparison: Implications For The Nature of ’Fold Space’, And Structure And Function Prediction. Curr. Opin. Struct. Biol. 16, 393–398 (2006)
Zheng, W.M.: The Use of A Conformational Alphabet for Fast Alignment of Protein Structures. In: Măndoiu, I., Wang, S.-L., Zelikovsky, A. (eds.) ISBRA 2008. LNCS (LNBI), vol. 4983, pp. 331–342. Springer, Heidelberg (2008)
Friedberg, I., Harder, T., Kolodny, R., Sitbon, E., Li, Z., Godzik, A.: Using An Alignment of Fragment Strings for Comparing Protein Structures. Bioinformatics 23, 219–224 (2007)
Holm, L., Kaariainen, S., Rosenstrom, P., Schenkel, A.: Searching Protein Structure Databases with DaliLite v.3. Bioinformatics 24, 2780–2781 (2008)
Margraf, T., Schenk, G., Torda, A.E.: The SALAMI Protein Structure Search Server. Nucleic. Acids. Res. 37, 480–484 (2009)
Usha, R., Murthy, M.R.: Protein Structural Homology: A Metric Approach. Int. J. Pept. Protein Res. 28(4), 364–369 (1986)
Abraham, A.L., Rocha, E.P., Pothier, J.: Swelfe: A Detector of Internal Repeats in Sequences and Structures. Bioinformatics 24(13), 1536–1537 (2008)
Sabarinathan, R., Basu, R., Sekar, K.: ProSTRIP: A Method to Find Similar Structural Repeats In Three-Dimensional Protein Structures. Comput. Biol. Chem. 34(2), 126–130 (2010)
Krissinel, E., Henrick, K.: Secondary-structure Matching (Ssm), A New Tool for Fast Protein Structure Alignment in Three Dimensions. Acta Cryst. D60, 2256–2268 (2004)
Wang, G., Dunbrack Jr., R.L.: PISCES: A Protein Sequence Culling Server. Bioinformatics 19(12), 1589–1591 (2003)
Eddy, S.R.: What Is Dynamic Programming? Nat. Biotechnol. 22, 909–910 (2004)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2012 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Rohit, S. et al. (2012). As3p: A Fast Algorithm to Search Structurally Similar Proteins. In: Huang, DS., Gupta, P., Zhang, X., Premaratne, P. (eds) Emerging Intelligent Computing Technology and Applications. ICIC 2012. Communications in Computer and Information Science, vol 304. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-31837-5_24
Download citation
DOI: https://doi.org/10.1007/978-3-642-31837-5_24
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-31836-8
Online ISBN: 978-3-642-31837-5
eBook Packages: Computer ScienceComputer Science (R0)