FlexSnap: flexible non-sequential protein structure alignment

Authors:
Saeed Salem;Mohammed J. Zaki;Chris Bystroff
Affiliations:
Department of Computer Science, Rensselaer Polytechnic Institute, Troy, NY;Department of Computer Science, Rensselaer Polytechnic Institute, Troy, NY;Department of Computer Science and Department of Biology, Rensselaer Polytechnic Institute, Troy, NY
Venue:
WABI'09 Proceedings of the 9th international conference on Algorithms in bioinformatics
Year:
2009

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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.