ArticleDigital discovery2024
iSIM: instant similarity.
Article in Digital discovery, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed.
- Efficient visualization of chemical space.Chemical science · 2026Article
- Pathway representationDigital discovery · 2026Article
- Undersampling Techniques for Nonlinear Chemical Space Visualization.Molecular informatics · 2026Article
- Development of Machine-Learned Interatomic Potentials to Predict Structure, Transport, and Reactivity in Platinum-Based Fuel Cells.ACS omega · 2026Article
- The (r)evolution of chemical space and molecular modeling: a time-resolved perspective.Journal of computer-aided molecular design · 2026Review
- 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
- ChemBang: Expanding the Chemical Space Around Small Molecules.Molecular informatics · 2026Article
- Divide and Cluster: The DIVINE Framework for Deterministic Top-Down Analysis of Molecular Dynamics Trajectories.Journal of chemical information and modeling · 2026Article
- Best practices to cluster large molecular libraries.bioRxiv : the preprint server for biology · 2026Article
- Article
- 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
- MetAP DB and Metal-FP: a database and fingerprint framework for advancing metal-based drug discovery.Journal of computer-aided molecular design · 2025Article
- Selector: A General Python Library for Diverse Subset Selection.bioRxiv : the preprint server for biology · 2025Article
- BitBIRCH-Lean: chemical space in the palm of your workstation.bioRxiv : the preprint server for biology · 2025Article
- Undersampling techniques for large datasets.bioRxiv : the preprint server for biology · 2025Article
- Efficiently finding activity cliffs.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
- iSIM-Sigma: Efficient Standard Deviation Calculation for Molecular Similarity.Journal of chemical information and modeling · 2025Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
The quantification of molecular similarity has been present since the beginning of cheminformatics. Although several similarity indices and molecular representations have been reported, all of them ultimately reduce to the calculation of molecular similarities of only two objects at a time. Hence, to obtain the average similarity of a set of molecules, all the pairwise comparisons need to be computed, which demands a quadratic scaling in the number of computational resources. Here we propose an exact alternative to this problem: iSIM (instant similarity). iSIM performs comparisons of multiple molecules at the same time and yields the same value as the average pairwise comparisons of molecules represented by binary fingerprints and real-value descriptors. In this work, we introduce the mathematical framework and several applications of iSIM in chemical sampling, visualization, diversity selection, and clustering.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.