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Flexible structure AlignmenT by Chaining Aligned fragment pairs allowing Twists

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Introduction Protein structures are flexible and undergo structural rearrangements as part of their function. FATCAT (Flexible structure AlignmenT by Chaining Aligned fragment pairs allowing Twists) is an approach for flexible protein structure comparison. It simultaneously addresses the two major goals of flexible structure alignment; optimizing the alignment and minimizing the number of rigid-body movements (twists) around pivot points (hinges) introduced in the reference structure. In FATCAT, the structure alignment is formulated as the AFPs (aligned fragment pairs) chaining process allowing at most t twists, and the flexible structure alignment is transformed into a rigid structure alignment when t is forced to be 0. Dynamic programming is used to find the optimal chaining.
Documents Algorithm paper; FATCAT report; FATCAT benchmarking
Reference Yuzhen Ye & Adam Godzik. Flexible structure alignment by chaining aligned fragment pairs allowing twists. 2003. Bioinformatics vol.19 suppl. 2. ii246-ii255. (more)
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bNAber: database of broadly neutralizing HIV antibodies. Alexey M. Eroshkin, Andrew LeBlanc, Dana Weekes, Kai Post, Zhanwen Li, Akhil Rajput, Sal T. Butera, Dennis R. Burton, Adam Godzik. Nucl. Acids Res.2013; published at http://nar.oxfordjournals.org on November 7, 2013 (10.1093/nar/gkt1083). Website: bnaber.org

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Current support provided by
NIH grant GM101457 - Development of the Flexible Comparative Modeling Toolkit

Previous supports provided by
NSF grant DBI-0349600, NIH grant GM63208 and NIH grant GM076221