ArticleJournal of cheminformatics2021
Extended similarity indices: the benefits of comparing more than two objects simultaneously. Part 2: speed, consistency, diversity selection.
Article in Journal of cheminformatics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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Who cites it
35 citing papers in PubMed.
- Efficient visualization of chemical space.Chemical science · 2026Article
- MSI: A Mahalanobis-Based Molecular Similarity Index for High-Dimensional Embeddings.Molecular informatics · 2026Article
- Undersampling Techniques for Nonlinear Chemical Space Visualization.Molecular informatics · 2026Article
- Pathway Representation via Intrinsic Structural Medoids (PRISM): A Structural Mapping Approach to Clustering Molecular Pathways.bioRxiv : the preprint server for biology · 2026Article
- ScalingJournal of chemical information and modeling · 2026Article
- mdBIRCH for Fast, Scalable, Online Clustering of Molecular Dynamics Trajectories.Journal of chemical theory and computation · 2026Article
- Divide and Cluster: The DIVINE Framework for Deterministic Top-Down Analysis of Molecular Dynamics Trajectories.Journal of chemical information and modeling · 2026Article
- Interpretable and Scalable Similarity Metrics for DNA-Encoded Library Design Using Generative Topographic Mapping.Molecular informatics · 2026Article
- Selector: A General Python Library for Diverse Subset Selection.Journal of chemical information and modeling · 2026Article
- Selector: A General Python Library for Diverse Subset Selection.bioRxiv : the preprint server for biology · 2025Article
- mdBIRCH for Fast, Scalable, Online Clustering of Molecular Dynamics Trajectories.bioRxiv : the preprint server for biology · 2025Article
- BitBIRCH-Lean: chemical space in the palm of your workstation.bioRxiv : the preprint server for biology · 2025Article
- Boosting Antibiotic Efficacy of Azole Drugs against Methicillin-Resistant Staphylococcus Aureus by Coordination to Rhenium Carbonyl Complexes.Chembiochem : a European journal of chemical biology · 2025Article
- CADENCE: Clustering Algorithm─Density-Based Exploration and Novelty Clustering with Efficiency.Journal of chemical information and modeling · 2025Article
- Hierarchical Extended Linkage Method (HELM)'s Deep Dive into Hybrid Clustering Strategies.Journal of chemical information and modeling · 2025Article
- iCliff Taylor's Version: Robust and Efficient Activity Cliff Determination.Journal of chemical information and modeling · 2025Article
- SHINE: Deterministic Many-to-Many Clustering of Molecular Pathways.Journal of chemical information and modeling · 2025Article
- Extended Quality (eQual): Radial Threshold Clustering Based onJournal of chemical information and modeling · 2025Article
- Extended Activity Cliffs-Driven Approaches on Data Splitting for the Study of Bioactivity Machine Learning Predictions.Molecular informatics · 2025Article
- Molecular similarity: Theory, applications, and perspectives.Artificial intelligence chemistry · 2024Article
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4 authors.
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Abstract
Despite being a central concept in cheminformatics, molecular similarity has so far been limited to the simultaneous comparison of only two molecules at a time and using one index, generally the Tanimoto coefficent. In a recent contribution we have not only introduced a complete mathematical framework for extended similarity calculations, (i.e. comparisons of more than two molecules at a time) but defined a series of novel idices. Part 1 is a detailed analysis of the effects of various parameters on the similarity values calculated by the extended formulas. Their features were revealed by sum of ranking differences and ANOVA. Here, in addition to characterizing several important aspects of the newly introduced similarity metrics, we will highlight their applicability and utility in real-life scenarios using datasets with popular molecular fingerprints. Remarkably, for large datasets, the use of extended similarity measures provides an unprecedented speed-up over "traditional" pairwise similarity matrix calculations. We also provide illustrative examples of a more direct algorithm based on the extended Tanimoto similarity to select diverse compound sets, resulting in much higher levels of diversity than traditional approaches. We discuss the inner and outer consistency of our indices, which are key in practical applications, showing whether the n-ary and binary indices rank the data in the same way. We demonstrate the use of the new n-ary similarity metrics on t-distributed stochastic neighbor embedding (t-SNE) plots of datasets of varying diversity, or corresponding to ligands of different pharmaceutical targets, which show that our indices provide a better measure of set compactness than standard binary measures. We also present a conceptual example of the applicability of our indices in agglomerative hierarchical algorithms. The Python code for calculating the extended similarity metrics is freely available at: https://github.com/ramirandaq/MultipleComparisons.
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