Protein Structure Comparison and Alignment Using Residue Contexts

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Protein Structure Comparison and Alignment Using Residue Contexts
We introduce a method for comparing protein structures using the notion of residue contexts based on protein Cα-atom backbones. The residue context is derived from the set of vectors from a given Cα-atom to each other Cα-atom in the molecule. A threedimensional histogram is generated from these vectors, containing a relative distribution of the other Cα-atoms for each Cα-atom on the backbone for a protein. Histograms are compared using the χ2 test, resulting in the cost for matching any two given Cαatoms in a pair of protein molecules. An optimal alignment is made using the Smith-Waterman algorithm, and a score is calculated based on the length of the alignment and the RMSD, yielding a best alignment that can be displayed in an interactive user interface. Resulting alignments are compared with alignments generated by CTSS, DALI, and CE, yielding different aligned protein regions.
Tobias Sayre, Rahul Singh
Added 29 May 2010
Updated 29 May 2010
Type Conference
Year 2008
Where AINA
Authors Tobias Sayre, Rahul Singh
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