Flexible structure alignment by chaining aligned fragment pairs allowing twists
نویسندگان
چکیده
منابع مشابه
Flexible structure alignment by chaining aligned fragment pairs allowing twists
MOTIVATION Protein structures are flexible and undergo structural rearrangements as part of their function, and yet most existing protein structure comparison methods treat them as rigid bodies, which may lead to incorrect alignment. RESULTS We have developed the Flexible structure AlignmenT by Chaining AFPs (Aligned Fragment Pairs) with Twists (FATCAT), a new method for structural alignment ...
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SUMMARY Popular methods for 3D protein structure similarity searching, especially those that generate high-quality alignments such as Combinatorial Extension (CE) and Flexible structure Alignment by Chaining Aligned fragment pairs allowing Twists (FATCAT) are still time consuming. As a consequence, performing similarity searching against large repositories of structural data requires increased ...
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We have recently developed a flexible protein structure alignment program (FATCAT) that identifies structural similarity, at the same time accounting for flexibility of protein structures. One of the most important applications of a structure alignment method is to aid in functional annotations by identifying similar structures in large structural databases. However, none of the flexible struct...
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Summary: CLeFAPS, a fast and flexible pairwise structural alignment algorithm based on a rigid-body framework, namely CLePAPS, is proposed. Instead of allowing twists (or bends), the flexible in CLeFAPS means: (a) flexibilization of the algorithm’s parameters through self-adapting with the input structures’ size, (b) flexibilization of adding the aligned fragment pairs (AFPs) into an one-to-mul...
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In the segment-based approach to sequence alignment. nucleic acid, and protein sequence alignments are constructed from fragments, i.e., from pairs of ungapped segments of the input sequences. Given a set F of candidate fragments and a weighting function w : F + FL:, the score of an alignment is defined as the sum of weights of the fragments it consists of. and the optimization problem is to fi...
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ژورنال
عنوان ژورنال: Bioinformatics
سال: 2003
ISSN: 1367-4803,1460-2059
DOI: 10.1093/bioinformatics/btg1086