tailieunhanh - Báo cáo sinh học: "FlexSnap: Flexible Non-sequential Protein Structure Alignment Research"

Tuyển tập các báo cáo nghiên cứu về sinh học được đăng trên tạp chí y học Molecular Biology cung cấp cho các bạn kiến thức về ngành sinh học đề tài: FlexSnap: Flexible Non-sequential Protein Structure Alignment Research. | Salem et al. Algorithms for Molecular Biology 2010 5 12 http content 5 1 12 AMR ALGORITHMS FOR ID MOLECULAR BIOLOGY RESEARCH Open Access FlexSnap Flexible Non-sequential Protein Structure Alignment Saeed Salem 1 Mohammed J Zaki2 and Chris Bystroff3 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 nonsequential 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. Availability An implementation of the FlexSnap algorithm will be made available online at http zaki software flexsnap. Background The wide spectrum of functions performed by proteins are enabled by their .

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