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Published on: August 13, 2020
Improving graphs of cycles approach to structural similarity of molecules
Stefi Nouleho Ilemo1, Dominique Barth1, Olivier David2
1DAVID, Department of Computer Science, University of Versailles Saint Quentin, Versailles, France.
Abstract:
This paper focuses on determining the structural similarity of two molecules, i.e., the similarity of the interconnection of all the elementary cycles in the corresponding molecular graphs. In this paper, we propose and analyze an algorithmic approach based on the resolution of the Maximum Common Edge Subgraph (MCES) problem with graphs representing the interaction of cycles molecules. Using the ChEBI database, we compare the effectiveness of this approach in terms of structural similarity and computation time with two calculations of similarity of molecular graphs, one based on the MCES, the other on the use of different fingerprints (Daylight, ECFP4, ECFP6, FCFP4, FCFP6) to measure Tanimoto coefficient. We also analyze the obtained structural similarity results for a selected subset of molecules.
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