ArticleJournal of cheminformatics2020
The rcdk and cluster R packages applied to drug candidate selection.
Article in Journal of cheminformatics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- Systematic metaproteomics mapping reveals functional and ecological landscapes of Ex vivo human gut microbiota responses to therapeutic drugs.Nature communications · 2025Article
- Structural Similarity, Activity, and Toxicity of Mycotoxins: Combining Insights from Unsupervised and Supervised Machine Learning Algorithms.Journal of agricultural and food chemistry · 2025Article
- Developmental toxicity of alkylated PAHs and substituted phenanthrenes: Structural nuances drive diverse toxicity and AHR activation.Chemosphere · 2025Article
- Unveiling the Anti-Obesity Potential of Thunder God Vine: Network Pharmacology and Computational Insights into Celastrol-like Molecules.International journal of molecular sciences · 2024Article
- Syn-COM: A Multi-Level Predictive Synergy Framework for Innovative Drug Combinations.Pharmaceuticals (Basel, Switzerland) · 2024Article
- sc2MeNetDrug: A computational tool to uncover inter-cell signaling targets and identify relevant drugs based on single cell RNA-seq data.PLoS computational biology · 2024Article
- Discovering Potential Compounds for Venous Disease Treatment through Virtual Screening and Network Pharmacology Approach.Molecules (Basel, Switzerland) · 2023Article
- Article
- Data-Driven Approaches Used for Compound Library Design for the Treatment of Parkinson's Disease.International journal of molecular sciences · 2023Article
- Big data and artificial intelligence (AI) methodologies for computer-aided drug design (CADD).Biochemical Society transactions · 2022Article
- Identification of a Quinone Derivative as a YAP/TEAD Activity Modulator from a Repurposing Library.Pharmaceutics · 2022Article
- Elucidating the Synergistic Effect of Multiple Chinese Herbal Prescriptions in the Treatment of Post-stroke Neurological Damage.Frontiers in pharmacology · 2022Article
- Repurposing the Trypanosomatidic GSK Kinetobox for the Inhibition of Parasitic Pteridine and Dihydrofolate Reductases.Pharmaceuticals (Basel, Switzerland) · 2021Article
- Automated Exploration of Prebiotic Chemical Reaction Space: Progress and Perspectives.Life (Basel, Switzerland) · 2021Review
- A direct-to-biology high-throughput chemistry approach to reactive fragment screening.Chemical science · 2021Article
- Chemoinformatic Screening for the Selection of Potential Senolytic Compounds from Natural Products.Biomolecules · 2021Article
- Scaffold Searching of FDA and EMA-Approved Drugs Identifies Lead Candidates for Drug Repurposing in Alzheimer's Disease.Frontiers in chemistry · 2021Article
- Z-matrix template-based substitution approach for enumeration of 3D molecular structures.MethodsX · 2021Article
- Learning cheminformatics.Journal of cheminformatics · 2020Article
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The aim of this article is to show how thevpower of statistics and cheminformatics can be combined, in R, using two packages: rcdk and cluster.We describe the role of clustering methods for identifying similar structures in a group of 23 molecules according to their fingerprints. The most commonly used method is to group the molecules using a "score" obtained by measuring the average distance between them. This score reflects the similarity/non-similarity between compounds and helps us identify active or potentially toxic substances through predictive studies.Clustering is the process by which the common characteristics of a particular class of compounds are identified. For clustering applications, we are generally measure the molecular fingerprint similarity with the Tanimoto coefficient. Based on the molecular fingerprints, we calculated the molecular distances between the methotrexate molecule and the other 23 molecules in the group, and organized them into a matrix. According to the molecular distances and Ward 's method, the molecules were grouped into 3 clusters. We can presume structural similarity between the compounds and their locations in the cluster map. Because only 5 molecules were included in the methotrexate cluster, we considered that they might have similar properties and might be further tested as potential drug candidates.
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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.