Protein structure comparison using bipartite graph matching and its application to protein structure classification.

William R Taylor

doi:10.1074/mcp.t200001-mcp200

Abstract

A measure of protein structure similarity is calculated from the matching of pairs of secondary structure elements between two proteins. The interaction of each pair was estimated from their axial line segments and combined with other geometric features to produce an optimal discrimination between intrafamily and interfamily relationships. The matching used a fast bipartite graph-matching algorithm that avoids the computational complexity of searching for the full subgraph isomorphism between the two sets of interactions. The main algorithm used was the "stable marriage" algorithm, which works on the ranked "preferences" of one interaction for another. The method takes 1/10 of a second for a typical comparison making it suitable as a fast pre-filter for slower, more exhaustive approaches. An application to protein structure classification is described.

Highlights

A measure of protein structure similarity is calculated from the matching of pairs of secondary structure elements between two proteins
The level of description of protein structure at which the greatest simplification can be achieved with the least loss of important topological information is when secondary structure elements (SSEs)1 are represented as line segments
Algorithm Execution Times—The execution time for the core matching algorithm was measured by running the pro

Summary

Introduction

A measure of protein structure similarity is calculated from the matching of pairs of secondary structure elements between two proteins. The matching of protein SSEs is approached using the simpler class of bipartite graph-matching algorithms These are designed to find an optimal pairing-up of SSEs, but do not attempt to constrain these in a coherent network as is required in the isomorphism algorithms. The level of description of protein structure at which the greatest simplification can be achieved with the least loss of important topological information is when secondary structure elements (SSEs) are represented as line segments This gives an order-of-magnitude reduction in the volume of data, which in some algorithms can lead to significant increases in speed [6, 7].

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Conclusion