Algorithm 457: finding all cliques of an undirected graph
Communications of the ACM
gSpan: Graph-Based Substructure Pattern Mining
ICDM '02 Proceedings of the 2002 IEEE International Conference on Data Mining
MoSS: a program for molecular substructure mining
Proceedings of the 1st international workshop on open source data mining: frequent pattern mining implementations
Determining Molecular Similarity for Drug Discovery using the Wavelet Riemannian Metric
BIBE '06 Proceedings of the Sixth IEEE Symposium on BionInformatics and BioEngineering
An Efficient Branch-and-bound Algorithm for Finding a Maximum Clique with Computational Experiments
Journal of Global Optimization
Bioinformatics
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Properties of a chemical entity, both physical and biological, are related to its structure. Since compound similarity can be used to infer properties of novel compounds, in chemoinformatics much attention has been paid to ways of calculating structural similarity. A useful metric to capture the structural similarity between compounds is the relative size of the Maximum Common Subgraph MCS. The MCS is the largest substructure present in a pair of compounds, when represented as graphs. However, in practice it is difficult to employ such a metric, since calculation of the MCS becomes computationally intractable when it is large. We propose a novel algorithm that significantly reduces computation time for finding large MCSs, compared to a number of state-of-the-art approaches. The use of this algorithm is demonstrated in an application predicting the transcriptional response of breast cancer cell lines to different drug-like compounds, at a scale which is challenging for the most efficient MCS-algorithms to date. In this application 714 compounds were compared.