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.

• Type: Conference
• Year: 2008
• Where: AINA
• Authors: Tobias Sayre, Rahul Singh
• Keywords: AINA 2008, Computer Networks, Protein, Protein Cα-atom Backbones, Residue Context