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Biophys Chem. 2014 Jun;190-191:50-5. doi: 10.1016/j.bpc.2014.01.005. Epub 2014 Feb 13.

A novel protein distance matrix based on the minimum arc-length between two amino-acid residues on the surface of a globular protein.

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  • 1Research School of Chemistry, Australian National University, Canberra ACT 0200, Australia; Immunology Frontier Research Center (IFReC), Section on Systems Immunology. Osaka University, 3-1 Yamada-oka, Suita, Osaka 565-0871, Japan. Electronic address: damien.hall@anu.edu.au.
  • 2Immunology Frontier Research Center (IFReC), Section on Systems Immunology. Osaka University, 3-1 Yamada-oka, Suita, Osaka 565-0871, Japan.
  • 3Research School of Chemistry, Australian National University, Canberra ACT 0200, Australia.
  • 4Immunology Frontier Research Center (IFReC), Section on Systems Immunology. Osaka University, 3-1 Yamada-oka, Suita, Osaka 565-0871, Japan. Electronic address: standley@ifrec.osaka-u.ac.jp.

Abstract

We present a novel protein distance matrix based on the minimum line of arc between two points on the surface of a protein. Two methods for calculating this distance matrix are developed and contrasted. The first method, which we have called TOPOL, is an approximate rule based algorithm consisting of successive rounds of vector addition. The second method is adapted from the graph theoretic approach of Dijkstra. Both procedures are demonstrated using cytochrome c, a 12,500 Da protein, as a test case. In respect to computational speed and accuracy the TOPOL procedure compares favorably against the more complex method based on shortest path enumeration over a surface manifold grid. Some potential uses of the algorithmic approaches and calculated surface protein distance measurement are discussed.

Copyright © 2014 Elsevier B.V. All rights reserved.

KEYWORDS:

Algorithm; Distance matrix; Protein–polymer interaction; Surface arc-length

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