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Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
Published on: July 16, 2017
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
Summary
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.
- 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.
