Nessa CarsonWho knew, when first starting a chemistry degree, that the humble hydrogen atom would give you more trouble than all the rest put together, yes, even the metals 😂 #chemoinformatics #chemistsWhoCode #chemchat
Cytology and GeneticsIdentification of Bacterial FtsZ Effectors Targeting the Sites of Coumarin Binding - #FtsZ #BP1 #BP2 #coumarins #ligandproteininteraction #chemoinformatics #pharmacophoresearch #moleculardocking #AI - https://link.springer.com/article/10.3103/S0095452725050056
Identification of Bacterial FtsZ Effectors Targeting the Sites of Coumarin Binding - Cytology and Genetics
Abstract— There is a large group of bacterial FtsZ inhibitors, the biological activity of which has been confirmed biochemically. However, the sites of protein-ligand interaction for most of them remain unknown, significantly complicating the further search and combinatorial design of FtsZ inhibitors. This study presents the results of bioinformatic analysis of bacterial FtsZ effectors targeting sites of 4-hydroxycoumarin binding (BP1 and BP2). New data based on original results of pharmacophore screening, chemoinformatics, molecular docking, molecular dynamics simulations, AI-predictions, etc., are presented. The object of the study was a combined library of 379 compounds, formed based on revision of the structural database RCSB Protein Data Bank and biochemically proven FtsZ effectors from ChEMBL. Based on the results of a comprehensive study, 39 compounds were selected, of which 28 were identified as effectors of the sites BP1 and BP2, and another 11 as specific effectors of the site BP2 located in the BP2/IDC superpocket.
Charles Tapley HoytI used chembl-downloader to create some nice charts on how the number of compounds, assays, activities, and other entities in ChEMBL have grown over time
📖 https://cthoyt.com/2025/08/26/chembl-history.html
#chembl #chemistry #chemometrics #chemoinformatics #cheminformatics #rdkit #cdk #proteochemometrics
A historical analysis of ChEMBL
I’ve recently submitted an article to the Journal of Open Source Software (JOSS) describing chembl-downloader, a Python package for automating downloading and using ChEMBL data in a reproducible way. In this post, I use chembl-downloader to show how the number of compounds, assays, activities, and other entities in ChEMBL have changed over time.
CSBJ🧪 Can AI revolutionize how we test chemicals for skin safety—without animal experiments?
🔗 SbD4Skin by EosCloud: Integrating multi-view molecular representation for predicting skin sensitization, irritation, and acute dermal toxicity. DOI: https://doi.org/10.1016/j.csbj.2025.08.001
📚 CSBJ Nanoscience and Advanced Materials: https://www.csbj.org/nano
#Toxicology #AI #SkinSafety #MachineLearning #Cosmetics #SbD4Skin #NoAnimalTesting #FAIRdata #Chemoinformatics #RegulatoryScience #QSAR #CSBJNAM @csbj
Most cheminformatics code that queries ChEMBL struggles with reproducibility.
chembl-downloader can help:
>>> import chembl_downloader as cd
>>> df = cd.query("""
SELECT chembl_id, pref_name
FROM molecule_dictionary
WHERE pref_name IS NOT NULL
""")
It's even sneaking its way into @wpwalters and @dr_greg_landrum blogs :)
Code/Docs: https://github.com/cthoyt/chembl-downloader
Preprint: https://arxiv.org/pdf/2507.17783
#cheminformatics #chemoinformatics #chembl #reproducibility #chemistry #openscience
Qiita - 人気の記事「メズマライザー」のPhosphoribosylaminoimidazolesuccinocarboxamideを再現する
https://qiita.com/aibio/items/ba3611365ce29945e318?utm_campaign=popular_items&utm_medium=feed&utm_source=popular_items
Bioinfo-fr.net📰 Introduction à la chémoinformatique : pour tout comprendre sur les bases de données de molécules et d'ingrédients 🧪 ⚗️ 👩🔬
https://bioinfo-fr.net/des-molecules-et-des-donnees
#bioinfofr #chemoinformatics
https://bioinfo-fr.net/des-molecules-et-des-donnees
#bioinfofr #chemoinformatics
Des molécules et des données ! - Bioinfo-fr.net
Vu que nous sommes sur un blog de bio-informatique, je vous propose aujourd'hui de parler chimie ! Enfin plutôt, chémoinformatique* et quelques notions de la façon dont une molécule est stockée en ligne en fonction des réglementations chimiques et cosmétiques. Je ne suis pas un expert de ce domaine, mais alors vraiment pas du tout. Par […]
Eric R. ScottMost exciting new feature in #rstats package {gt}? Pretty formatting of chemical formulae and chemical reactions
U of A CCT Data Science@redata And check out the corresponding R package we worked on if you want to calculate these volatility estimates on your own data: https://meredith-lab.github.io/volcalc/
Calculate Volatility of Chemical Compounds
Calculate estimated relative volatility index values for organic compounds based on functional group contributions. Calculation uses the SIMPOL.1 method in Prankow and Asher (2008) <doi:10.5194/acp-8-2773-2008> or modified SIMPOL.1 method as in Meredith et al. (2023) <doi:10.5194/acp-8-2773-2008>.
If you're interested in calculating estimated volatility for your own data, check out the R package we worked on for this project: https://meredith-lab.github.io/volcalc/
Calculate Volatility of Chemical Compounds
Calculate estimated relative volatility index values for organic compounds based on functional group contributions. Calculation uses the SIMPOL.1 method in Prankow and Asher (2008) <doi:10.5194/acp-8-2773-2008> or modified SIMPOL.1 method as in Meredith et al. (2023) <doi:10.5194/acp-8-2773-2008>.