ArticleJournal of cheminformatics2021
Extended similarity indices: the benefits of comparing more than two objects simultaneously. Part 1: Theory and characteristics
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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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
- 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
- Extended Quality (eQual): Radial Threshold Clustering Based onJournal of chemical information and modeling · 2025Article
- SHINE: Deterministic Many-to-Many Clustering of Molecular Pathways.Journal 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
- Alternative weighting schemes for fine-tuned extended similarity indices.Journal of chemometrics · 2024Article
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4 authors.
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Abstract
Quantification of the similarity of objects is a key concept in many areas of computational science. This includes cheminformatics, where molecular similarity is usually quantified based on binary fingerprints. While there is a wide selection of available molecular representations and similarity metrics, there were no previous efforts to extend the computational framework of similarity calculations to the simultaneous comparison of more than two objects (molecules) at the same time. The present study bridges this gap, by introducing a straightforward computational framework for comparing multiple objects at the same time and providing extended formulas for as many similarity metrics as possible. In the binary case (i.e. when comparing two molecules pairwise) these are naturally reduced to their well-known formulas. We provide a detailed analysis on the effects of various parameters on the similarity values calculated by the extended formulas. The extended similarity indices are entirely general and do not depend on the fingerprints used. Two types of variance analysis (ANOVA) help to understand the main features of the indices: (i) ANOVA of mean similarity indices; (ii) ANOVA of sum of ranking differences (SRD). Practical aspects and applications of the extended similarity indices are detailed in the accompanying paper: Miranda-Quintana et al. J Cheminform. 2021. https://doi.org/10.1186/s13321-021-00504-4 . Python code for calculating the extended similarity metrics is freely available at: https://github.com/ramirandaq/MultipleComparisons .
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