Skip to main content
Springer Nature Link
Log in

Protein Annotation by Secondary Structure Based Alignments (PASSTA)

  • Conference paper
Computational Life Sciences (CompLife 2005)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 3695))

Included in the following conference series:

  • 1046 Accesses

Abstract

Most software tools in homology recognition on proteins answer only a few specific questions, often leaving not much room for the interpretation of the results. We develop a software Passta that helps to decide whether a protein sequence is related to a protein with known structure. Our approach may indicate rearrangements and duplications, and it displays information from different sources in an integrated fashion.

Our approach is to first break each sequence of the Protein Data Bank (PDB) into Secondary Structure Elements (SSEs). Given a query sequence, our goal is then to ‘explain’ it by SSE sequences as good as possible. Therefore, we use the Waterman-Eggert algorithm to compute pairwise alignments of SSE sequences with the query. In a graph-based approach, we then select those alignments that reproduce the query in an optimal way. We discuss two examples to illustrate the potential (and possible pitfalls) of the method.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

Similar content being viewed by others

References

  1. Shi, J., Blundell, T.L., Mizuguchi, K.: FUGUE: Sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties. J. Mol. Biol. 310, 243–257 (2001)

    Article  Google Scholar 

  2. Altschul, S.F., Gish, W., Miller, W., Myers, E.W., Lipman, D.J.: Basic local alignment search tool. J. Mol. Biol. 215, 403–410 (1990)

    Google Scholar 

  3. Pearson, W.R.: Rapid and sensitive sequence comparison with FASTP and FASTA. In: Doolittle, R.F. (ed.) Molecular Evolution: Computer Analysis of Protein and Nucleic Acid Sequences. Meth. Enzymol., vol. 183, pp. 63–98. Academic Press, San Diego (1990)

    Google Scholar 

  4. Smith, T.F., Waterman, M.S.: Identification of common molecular subsequences. J. Mol. Biol. 147, 195–197 (1981)

    Article  Google Scholar 

  5. Altschul, S.F., Madden, T.L., Schäffer, A.A., Zhang, J., Zhang, Z., Miller, W., Lipman, D.J.: Gapped blast and psi-blast: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389–3402 (1997)

    Article  Google Scholar 

  6. Eddy, S.R.: Profile hidden Markov models. Bioinformatics 14, 755–763 (1998)

    Article  Google Scholar 

  7. Spang, R., Rehmsmeier, M., Stoye, J.: A novel approach to remote homology detection: Jumping alignments. J. Comp. Biol. 9, 747–760 (2002)

    Article  Google Scholar 

  8. Bannert, C.: Systematic investigation of jumping alignments. Technical Report 2003-05 (2003), http://www.cebitec.uni-bielefeld.de/~bannert/pubs.html

  9. Bourne, P.E., Weissig, H.: Structural Bioinformatics. Wiley Liss, Chichester (2003)

    Book  Google Scholar 

  10. Hubbard, T.J., Ailey, B., Brenner, S.E., Murzin, A.G., Chothia, C.: SCOP: A Structural Classification of Proteins database. Nucleic Acids Res. 27, 254–256 (1999)

    Article  Google Scholar 

  11. Murzin, A.G., Brenner, S.E., Hubbard, T., Chothia, C.: SCOP: A structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 247, 536–540 (1995)

    Google Scholar 

  12. Russell, R.B., Copley, R.R., Barton, G.J.: Protein fold recognition by mapping predicted secondary structures. J. Mol. Biol. 259, 349–365 (1996)

    Article  Google Scholar 

  13. Ye, Y., Jaroszewski, L., Li, W., Godzik, A.: A segment alignment approach to protein comparison. Bioinformatics 19, 742–749 (2003)

    Article  Google Scholar 

  14. Shih, E., Hwang, M.J.: Alternative alignments from comparison of protein structures. Proteins 56, 519–527 (2004)

    Article  Google Scholar 

  15. Kabsch, W., Sander, C.: Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22, 2577–2637 (1983)

    Article  Google Scholar 

  16. 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)

    Article  Google Scholar 

  17. May, P., Barthel, S., Koch, I.: Ptgl - a web-based database application for protein topologies. Bioinformatics 20, 3277–3279 (2004)

    Article  Google Scholar 

  18. Hooft, R.W.W., Sander, C., Vriend, G.: The pdbfinder database: A summary of pdb, dssp and hssp information with added value. CABIOS 12, 525–529 (1996)

    Google Scholar 

  19. Brenner, S.E., Koehl, P., Levitt, M.: The astral compendium for protein structure and sequence analysis. Nucleic Acids Res. 28, 254–256 (2000)

    Article  Google Scholar 

  20. Chandonia, J.M., Walker, N.S., Lo Conte, L., Koehl, P., Levitt, M., Brenner, S.E.: Astral compendium enhancements. Nucleic Acids Res. 30, 260–263 (2002)

    Article  Google Scholar 

  21. Waterman, M.S., Eggert, M.: A new algorithm for best subsequence alignments with application to trna-rrna comparisons. J. Mol. Biol. 197, 723–728 (1987)

    Article  Google Scholar 

  22. Cormen, T.H., Leiserson, C.E., Rivest, R.L., Stein, C.: Introduction to Algorithms, 2nd edn. MIT Press / McGraw-Hill, Cambridge (2001)

    MATH  Google Scholar 

  23. Pearl, F.M.G., Lee, D., Bray, J.E., Sillitoe, I., Todd, A.E., Harrison, A.P., Thornton, J.M., Orengo, C.A.: Assigning genomic sequences to cath. Nucleic Acids Res. 28, 277–282 (2000)

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Technische Fakultät, Universität Bielefeld, Germany

    Constantin Bannert & Jens Stoye

Authors
  1. Constantin Bannert
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Jens Stoye
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. Berkeley Initiative in Soft Computing (BISC), University of California at Berkeley, USA

    Michael R. Berthold

  2. Unilever Centre for Molecular Informatics, Department of Chemistry, Cambridge University, CB2 1EW, Cambridge, UK

    Robert C. Glen

  3. Department of Biology, University of Konstanz, Box M647, 78457, Konstanz, Germany

    Kay Diederichs

  4. Division for Simulation of Biological Systems, Center for Bioinformatics Tübingen, Eberhard Karls University Tübingen, 72076, Tübingen, Germany

    Oliver Kohlbacher

  5. ALTANA Chair for Bioinformatics and Information Mining, University of Konstanz, Germany

    Ingrid Fischer

Rights and permissions

Reprints and permissions

Copyright information

© 2005 Springer-Verlag Berlin Heidelberg

About this paper

Cite this paper

Bannert, C., Stoye, J. (2005). Protein Annotation by Secondary Structure Based Alignments (PASSTA). In: R. Berthold, M., Glen, R.C., Diederichs, K., Kohlbacher, O., Fischer, I. (eds) Computational Life Sciences. CompLife 2005. Lecture Notes in Computer Science(), vol 3695. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11560500_8

Download citation

  • DOI: https://doi.org/10.1007/11560500_8

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-29104-6

  • Online ISBN: 978-3-540-31726-5

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics

Search

Navigation