FlexSnap

Flexible non-sequential protein structure alignment

Saeed Salem, Mohammed J. Zaki, Chris Bystroff

Research output: Contribution to journalArticle

32 Citations (Scopus)

Abstract

Background: Proteins have evolved subject to energetic selection pressure for stability and flexibility. Structural similarity between proteins that 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 Sequential permutations are considered. We propose the FlexSnap algorithm for flexible non-topological protein structural alignment.Results: 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. Moreover on the DynDom dataset, FlexSnap reported longer alignments with smaller rmsd.Conclusions: We have introduced FlexSnap, a greedy chaining algorithm that reports both sequential and non-sequential alignments and allows twists (hinges). We assessed the quality of the FlexSnap alignments by measuring its agreements with manually curated non-sequential alignments. On the FlexProt dataset, FlexSnap was competitive to state-of-the-art flexible alignment methods. Moreover, we demonstrated the benefits of introducing hinges by showing significant improvements in the alignments reported by FlexSnap for the structure pairs for which rigid alignment methods reported alignments with either low coverage or large rmsd.

Original languageEnglish
Article number12
JournalAlgorithms for Molecular Biology
Volume5
Issue number1
DOIs
Publication statusPublished - 4 Jan 2010
Externally publishedYes

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Protein Structure
Alignment
Proteins
Secondary Protein Structure
Protein
Pressure
Flexibility
Hinges
Structural Similarity
Datasets
Secondary Structure
Greedy Algorithm
Twist
Packing
Permutation
Coverage

ASJC Scopus subject areas

  • Computational Theory and Mathematics
  • Applied Mathematics
  • Molecular Biology
  • Structural Biology

Cite this

FlexSnap : Flexible non-sequential protein structure alignment. / Salem, Saeed; Zaki, Mohammed J.; Bystroff, Chris.

In: Algorithms for Molecular Biology, Vol. 5, No. 1, 12, 04.01.2010.

Research output: Contribution to journalArticle

Salem, Saeed ; Zaki, Mohammed J. ; Bystroff, Chris. / FlexSnap : Flexible non-sequential protein structure alignment. In: Algorithms for Molecular Biology. 2010 ; Vol. 5, No. 1.
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