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

- A novel protein distance matrix based on surface residue arc-length is discussed.
- Two methods for calculating the protein distance matrix for globular proteins are presented.
- The simpler of the two methods, based on a rule-based algorithm, was found to yield suitable results.

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.