ArticleJournal of computer-aided molecular design2022
Progress on open chemoinformatic tools for expanding and exploring the chemical space.
Article in Journal of computer-aided molecular design, 2022. 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.
- Undersampling Techniques for Nonlinear Chemical Space Visualization.Molecular informatics · 2026Article
- CRUSH-Cleavage Rules Using SMIRKS Heuristics: an enhanced molecular fragmentation algorithm.Journal of cheminformatics · 2026Article
- How far can you go? Extrapolating values of catalytic activity from known protein landscapes in natural and directed evolution.Chemical Society reviews · 2026Review
- Chemical space visualization at scale: a survey of end-to-end pipelines and dataset-size archetypes.Journal of cheminformatics · 2026Review
- A Reinforcement Learning-Guided Genetic Algorithm Integrating Medicinal Chemistry-Inspired Molecular Transformations.Journal of chemical information and modeling · 2026Article
- IRACEMA: A Database Management System for Bioactive Compounds Obtained and Characterized by Brazilian Researchers.ACS omega · 2026Article
- Discovery of hybrid chemical synthesis pathways with DORAnet.Digital discovery · 2025Article
- Growth vs Diversity: A Time-Evolution Analysis of the Chemical Space.Journal of chemical information and modeling · 2025Article
- An evaluation methodology for machine learning-based tandem mass spectra similarity prediction.BMC bioinformatics · 2025Article
- Machine learning-based bioactivity prediction of porphyrin derivatives: molecular descriptors, clustering, and model evaluation.Photochemical & photobiological sciences : Official journal of the European Photochemistry Association and the European Society for Photobiology · 2025Article
- Cheminformatics Approaches to the Analysis of Additives for Sustainable Polymeric Materials.Polymers · 2025Article
- Molecular similarity: Theory, applications, and perspectives.Artificial intelligence chemistry · 2024Article
- Unlocking marine microbial treasures: new PBP2a-targeted antibiotics elicited by metals and enhanced by RSM-driven transcriptomics and chemoinformatics.Microbial cell factories · 2024Article
- MolCompass: multi-tool for the navigation in chemical space and visual validation of QSAR/QSPR models.Journal of cheminformatics · 2024Article
- One chiral fingerprint to find them all.Journal of cheminformatics · 2024Article
- Making sense of chemical space network shows signs of criticality.Scientific reports · 2023Article
- Art driven by visual representations of chemical space.Journal of cheminformatics · 2023Article
- Alchemical analysis of FDA approved drugs.Digital discovery · 2023Article
- Machine learning prediction of empirical polarity using SMILES encoding of organic solvents.Molecular diversity · 2023Article
- Sampling and Mapping Chemical Space with Extended Similarity Indices.Molecules (Basel, Switzerland) · 2023Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
The concept of chemical space is a cornerstone in chemoinformatics, and it has broad conceptual and practical applicability in many areas of chemistry, including drug design and discovery. One of the most considerable impacts is in the study of structure-property relationships where the property can be a biological activity or any other characteristic of interest to a particular chemistry discipline. The chemical space is highly dependent on the molecular representation that is also a cornerstone concept in computational chemistry. Herein, we discuss the recent progress on chemoinformatic tools developed to expand and characterize the chemical space of compound data sets using different types of molecular representations, generate visual representations of such spaces, and explore structure-property relationships in the context of chemical spaces. We emphasize the development of methods and freely available tools focusing on drug discovery applications. We also comment on the general advantages and shortcomings of using freely available and easy-to-use tools and discuss the value of using such open resources for research, education, and scientific dissemination.
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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.