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FlexSnap: flexible non-sequential protein structure alignment.

Saeed Salem1, Mohammed J Zaki, Chris Bystroff

  • 1Department of Computer Science, North Dakota State University, Fargo, ND 58108, USA. saeed.salem@ndsu.edu

Algorithms for Molecular Biology : AMB
|January 6, 2010
PubMed
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FlexSnap is a novel algorithm for flexible protein structural alignment. It effectively identifies similarities between proteins, even with conformational changes or sequential permutations, outperforming existing methods.

Area of Science:

  • Computational Biology
  • Structural Bioinformatics
  • Protein Structure Analysis

Background:

  • Proteins evolve under energetic pressures for stability and flexibility.
  • Considering protein flexibility is crucial for capturing structural similarity in proteins with conformational changes.
  • Flexibility and sequential permutations enable detection of topologically unrelated proteins preserving secondary structure packing.

Purpose of the Study:

  • To introduce the FlexSnap algorithm for flexible non-topological protein structural alignment.
  • To enable detection of both sequential and non-sequential structural alignments, including twists (hinges).

Main Methods:

  • Developed FlexSnap, a greedy chaining algorithm.
  • Assessed alignment quality by comparing with manually curated non-sequential structural alignments.

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  • Evaluated performance against state-of-the-art algorithms like DALI, SARF2, MultiProt, FlexProt, and FATCAT.

    • Main Results:

    • FlexSnap demonstrated competitive results against leading algorithms.
    • On the DynDom dataset, FlexSnap achieved longer alignments with smaller root-mean-square deviation (rmsd).
    • Significant improvements were observed for structure pairs where rigid alignment methods failed.

    Conclusions:

    • FlexSnap is a versatile algorithm for flexible protein alignment, handling sequential and non-sequential structures with hinges.
    • The algorithm's effectiveness is validated against established methods and manual alignments.
    • FlexSnap offers enhanced alignment capabilities, particularly for complex protein structures.