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FlexSnap: Flexible Non-sequential Protein Structure Alignment

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Algorithms in Bioinformatics (WABI 2009)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 5724))

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Abstract

Proteins have evolved subject to energetic selection pressure for stability and flexibility. Structural similarity between proteins which have gone through conformational changes can be captured effectively if flexibility is considered. Topologically unrelated proteins that preserve secondary structure packing interactions can be detected if both flexibility and sequence permutations are considered. We propose the FlexSnap algorithm for flexible non-topological protein structural alignment. The effectiveness of FlexSnap is demonstrated by measuring the agreement of its alignments with manually curated non-sequential structural alignments. FlexSnap showed competitive results against state-of-the-art algorithms, like DALI, SARF2, MultiProt, FlexProt, and FATCAT.

This work was supported in part by NSF Grants EMT-0829835, and CNS-0103708, and NIH Grant 1R01EB0080161-01A1.

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Authors and Affiliations

  1. Department of Computer Science, USA

    Saeed Salem, Mohammed J. Zaki & Chris Bystroff

  2. Department of Biology, Rensselaer Polytechnic Institute, Troy NY, 12180, USA

    Chris Bystroff

Authors
  1. Saeed Salem
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  2. Mohammed J. Zaki
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  3. Chris Bystroff
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Editor information

Editors and Affiliations

  1. Center for Bioinformatics and Computational Biology, and Department of Computer Science, University of Maryland, MD, College Park, USA

    Steven L. Salzberg

  2. Department of Computer Sciences, The University of Texas at Austin, TX, USA

    Tandy Warnow

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© 2009 Springer-Verlag Berlin Heidelberg

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Salem, S., Zaki, M.J., Bystroff, C. (2009). FlexSnap: Flexible Non-sequential Protein Structure Alignment. In: Salzberg, S.L., Warnow, T. (eds) Algorithms in Bioinformatics. WABI 2009. Lecture Notes in Computer Science(), vol 5724. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-04241-6_23

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  • DOI: https://doi.org/10.1007/978-3-642-04241-6_23

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-04240-9

  • Online ISBN: 978-3-642-04241-6

  • eBook Packages: Computer ScienceComputer Science (R0)

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