Dataset Information

ChemMaps: Towards an approach for visualizing the chemical space based on adaptive satellite compounds.

ABSTRACT: We present a novel approach called ChemMaps for visualizing chemical space based on the similarity matrix of compound datasets generated with molecular fingerprints' similarity. The method uses a 'satellites' approach, where satellites are, in principle, molecules whose similarity to the rest of the molecules in the database provides sufficient information for generating a visualization of the chemical space. Such an approach could help make chemical space visualizations more efficient. We hereby describe a proof-of-principle application of the method to various databases that have different diversity measures. Unsurprisingly, we found the method works better with databases that have low 2D diversity. 3D diversity played a secondary role, although it seems to be more relevant as 2D diversity increases. For less diverse datasets, taking as few as 25% satellites seems to be sufficient for a fair depiction of the chemical space. We propose to iteratively increase the satellites number by a factor of 5% relative to the whole database, and stop when the new and the prior chemical space correlate highly. This Research Note represents a first exploratory step, prior to the full application of this method for several datasets.

SUBMITTER: Naveja JJ

PROVIDER: S-EPMC5538041 | biostudies-literature | 2017

REPOSITORIES: biostudies-literature

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ChemMaps: Towards an approach for visualizing the chemical space based on adaptive satellite compounds.

Naveja J Jesús JJ Medina-Franco José L JL

F1000Research 20170717

We present a novel approach called ChemMaps for visualizing chemical space based on the similarity matrix of compound datasets generated with molecular fingerprints' similarity. The method uses a 'satellites' approach, where satellites are, in principle, molecules whose similarity to the rest of the molecules in the database provides sufficient information for generating a visualization of the chemical space. Such an approach could help make chemical space visualizations more efficient. We hereb ...[more]

PMID: 28794856

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Project description:Given a compound, how can we effectively predict its biological function? It is a fundamentally important problem because the information thus obtained may benefit the understanding of many basic biological processes and provide useful clues for drug design. In this study, based on the information of chemical-chemical interactions, a novel method was developed that can be used to identify which of the following eleven metabolic pathway classes a query compound may be involved with: (1) Carbohydrate Metabolism, (2) Energy Metabolism, (3) Lipid Metabolism, (4) Nucleotide Metabolism, (5) Amino Acid Metabolism, (6) Metabolism of Other Amino Acids, (7) Glycan Biosynthesis and Metabolism, (8) Metabolism of Cofactors and Vitamins, (9) Metabolism of Terpenoids and Polyketides, (10) Biosynthesis of Other Secondary Metabolites, (11) Xenobiotics Biodegradation and Metabolism. It was observed that the overall success rate obtained by the method via the 5-fold cross-validation test on a benchmark dataset consisting of 3,137 compounds was 77.97%, which is much higher than 10.45%, the corresponding success rate obtained by the random guesses. Besides, to deal with the situation that some compounds may be involved with more than one metabolic pathway class, the method presented here is featured by the capacity able to provide a series of potential metabolic pathway classes ranked according to the descending order of their likelihood for each of the query compounds concerned. Furthermore, our method was also applied to predict 5,549 compounds whose metabolic pathway classes are unknown. Interestingly, the results thus obtained are quite consistent with the deductions from the reports by other investigators. It is anticipated that, with the continuous increase of the chemical-chemical interaction data, the current method will be further enhanced in its power and accuracy, so as to become a useful complementary vehicle in annotating uncharacterized compounds for their biological functions.

Dataset Information

ChemMaps: Towards an approach for visualizing the chemical space based on adaptive satellite compounds.

Publications

ChemMaps: Towards an approach for visualizing the chemical space based on adaptive satellite compounds.

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