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The Use of a Conformational Alphabet for Fast Alignment of Protein Structures

  • Wei-Mou Zheng
Part of the Lecture Notes in Computer Science book series (LNCS, volume 4983)

Abstract

A protein conformational alphabet refers to the discretized states of the three-dimensional segmental structure of protein backbones. Here a letter corresponds to a cluster of combinations of three angles formed by C α pseudobonds of four contiguous residues, and our alphabet consist of 17 letters obtained by clustering based on the probability distribution of these angles. A substitution matrix called CLESUM has been derived from an alignment database of representative structures to measure both evolutionary and geometrical similarity between any two such letters. A structural fragment is then mapped to a string, and two strings with their CLESUM score being higher than a preset threshold form a similar fragment pair (SFP). The search for SFPs by string comparison is fast. Furthermore, CLESUM scores reflect the importance of SFPs to structure alignment, and then the search space can be significantly reduced. A fast tool for pairwise alignment called CLePAPS is developed by collecting as many spatially consistent SFPs as possible. Extending the concept of SFPs to that of similar fragment blocks for multiple structure alignment leads to a fast tool for multiple structure alignment called BLOMAPS. Both CLePAPS and BLOMAPS are tested on ensembles of various structures. They are reliable, and about two or three orders faster than some well-known algorithms.

Keywords

Structure Alignment Pairwise Alignment Substitution Matrix Fast Tool Protein Structure Alignment 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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References

  1. Dror, O., Benyamini, H., Nussinov, R., Wolfson, H.: MASS: Multiple structural alignment by secondary structures. Bioinformatics 19(suppl. 1), 95–104 (2003a)CrossRefGoogle Scholar
  2. Dror, O., Benyamini, H., Nussinov, R., Wolfson, H.: Multiple structural alignment by secondary structures: Algorithm and applications. Protein Science 12, 2492–2507 (2003b)CrossRefGoogle Scholar
  3. Fischer, D., Elofsson, A., Rice, D., Eisenberg, D.: Assessing the performance of fold recognition methods by means of a comprehensive benchmark. In: Proc. Pac. Symp. Biocomput., pp. 300–318 (1996)Google Scholar
  4. Gibrat, J.F., Madej, T., Bryant, S.H.: Surprising similarities in structure comparison. Current Opinion in Structural Biology 6, 377–385 (1996)CrossRefGoogle Scholar
  5. Guda, C., Lu, S., Sheeff, E.D., Bourne, P.E., Shindyalov, I.N.: CE-MC: A multiple protein structure alignment server. Nucleic Acids Res. 32, W100–W103 (2004)Google Scholar
  6. Holm, L., Sander, C.: Dali/FSSP classification of three-dimensional protein folds. Nucleic Acid Res. 25, 231–234 (1997)CrossRefGoogle Scholar
  7. Kabsch, W.: A discussion of the solution for the best rotation to related two sets of vectors. Acta. Crystal. 34A, 827–828 (1978)CrossRefGoogle Scholar
  8. Lackner, P., Koppensteiner, W.A., Sippl, M.J., Domingues, F.S.: ProSup: A refined tool for protein structure alignment. Protein Engineering 13, 745–752 (2000)CrossRefGoogle Scholar
  9. Lupyan, D., Leo-Macias, A., Ortiz, A.R.: A new progressive-iterative algorithm for multiple structure alignment. Bioinformatics 21, 3255–3263 (2005)CrossRefGoogle Scholar
  10. Shatsky, M., Nussinov, R., Wolfson, H.: MultiProt – A multiple protein structural alignment algorithm. In: Guigó, R., Gusfield, D. (eds.) WABI 2002. LNCS, vol. 2452, pp. 235–250. Springer, Heidelberg (2002)CrossRefGoogle Scholar
  11. Shindyalov, I.N., Bourne, P.E.: Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. Protein Engineering 11, 739–747 (1998)CrossRefGoogle Scholar
  12. Vriend, G., Sander, C.: Detection of common three-dimensional substructures in proteins. Proteins 11, 52–58 (1991)CrossRefGoogle Scholar
  13. Ye, J., Janardan, R.: Approximate Multiple Protein Structure Alignment Using the Sum-of-Pairs Distance. J. Comput. Biol. 11, 986–1000 (2004)CrossRefGoogle Scholar
  14. Zheng, W.M.: Relation between weight matrix and substitution matrix: Motif search by similarity. Bioinformatics 21, 938–943 (2005)CrossRefGoogle Scholar
  15. Zheng, W.M., Liu, X.: A protein structural alphabet and its substitution matrix CLESUM. In: Priami, C., Zelikovsky, A. (eds.) Transactions on Computational Systems Biology II. LNCS (LNBI), vol. 3680, pp. 59–67. Springer, Heidelberg (2005), http://arxiv.org/abs/q-bio/0412046 CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2008

Authors and Affiliations

  • Wei-Mou Zheng
    • 1
  1. 1.Institute of Theoretical Physics, Academia SinicaBeijingChina

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