ArticleJournal of cheminformatics2016
Scaffold analysis of PubChem database as background for hierarchical scaffold-based visualization.
Article in Journal of cheminformatics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed, 20 citations in OpenAlex.
- Structural diversity and chemical space analysis of a PROTAC database using unsupervised machine learning.Scientific reports · 2026Article
- Framework for evaluating explainable AI in antimicrobial drug discovery.Journal of cheminformatics · 2026Article
- Machine Learning-Driven Consensus Modeling for Activity Ranking and Chemical Landscape Analysis of HIV-1 Inhibitors.Pharmaceuticals (Basel, Switzerland) · 2025Article
- Evaluating the Diversity and Target Addressability of DELs using Scaffold Analysis and Machine Learning.ACS medicinal chemistry letters · 2025Article
- From High Dimensions to Human Insight: Exploring Dimensionality Reduction for Chemical Space Visualization.Molecular informatics · 2025Article
- Development of Activity Rules and Chemical Fragment Design for In Silico Discovery of AChE and BACE1 Dual Inhibitors against Alzheimer's Disease.Molecules (Basel, Switzerland) · 2023Article
- AddictedChem: A Data-Driven Integrated Platform for New Psychoactive Substance Identification.Molecules (Basel, Switzerland) · 2022Article
- Scalable estimator of the diversity for de novo molecular generation resulting in a more robust QM dataset (OD9) and a more efficient molecular optimization.Journal of cheminformatics · 2021Article
- Dataset's chemical diversity limits the generalizability of machine learning predictions.Journal of cheminformatics · 2019Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundVisualization of large molecular datasets is a challenging yet important topic utilised in diverse fields of chemistry ranging from material engineering to drug design. Especially in drug design, modern methods of high-throughput screening generate large amounts of molecular data that call for methods enabling their analysis. One such method is classification of compounds based on their molecular scaffolds, a concept widely used by medicinal chemists to group molecules of similar properties. This classification can then be utilized for intuitive visualization of compounds.
resultsIn this paper, we propose a scaffold hierarchy as a result of large-scale analysis of the PubChem Compound database. The analysis not only provided insights into scaffold diversity of the PubChem Compound database, but also enables scaffold-based hierarchical visualization of user compound data sets on the background of empirical chemical space, as defined by the PubChem data, or on the background of any other user-defined data set. The visualization is performed by a web based client-server application called Scaffvis. It provides an interactive zoomable tree map visualization of data sets up to hundreds of thousands molecules. Scaffvis is free to use and its source codes have been published under an open source license.Graphical abstract.
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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.