#chemoinformatics — Public Fediverse posts

Who 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

I 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

I 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

I 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

I 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

🧪 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

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

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

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

📰 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

Most exciting new feature in #rstats package {gt}? Pretty formatting of chemical formulae and chemical reactions

https://posit.co/blog/everything-new-thats-in-gt-0-11-0/

#chemoinformatics #metabolomics

@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/

#chemoinformatics #rstats #metabolomics

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/

https://mastodon.social/@redata/112735328621451622

#metabolomics #chemoinformatics

PhD student position in Life Science Informatics (50%)

University of Bonn

PhD student position in Chemoinformatics in the group of Prof. Bajorath (Bonn/Germany)

See the full job description on jobRxiv: https://jobrxiv.org/job/university-of-bonn-27779-phd-student-position-in-life-science-informatics-50/?feed_id=75466

#artificial_intelligence #chemoinformatics #computational_...
https://jobrxiv.org/job/university-of-bonn-27779-phd-student-position-in-life-science-informatics-50/?feed_id=75466

PhD student position in Life Science Informatics (50%)

University of Bonn

PhD student position in Chemoinformatics in the group of Prof. Bajorath (Bonn/Germany)

See the full job description on jobRxiv: https://jobrxiv.org/job/university-of-bonn-27779-phd-student-position-in-life-science-informatics-50/?feed_id=75249

#artificial_intelligence #chemoinformatics #computational_...
https://jobrxiv.org/job/university-of-bonn-27779-phd-student-position-in-life-science-informatics-50/?feed_id=75249

PhD student position in Life Science Informatics (50%)

University of Bonn

PhD student position in Chemoinformatics in the group of Prof. Bajorath (Bonn/Germany)

See the full job description on jobRxiv: https://jobrxiv.org/job/university-of-bonn-27779-phd-student-position-in-life-science-informatics-50/?feed_id=74941

#artificial_intelligence #chemoinformatics #computational_...
https://jobrxiv.org/job/university-of-bonn-27779-phd-student-position-in-life-science-informatics-50/?feed_id=74941

🎉🎉🎉 We're happy to announce the release of {volcalc} v2.1.0 along with the publication of an associated manuscript in Frontiers in Microbiology!

{volcalc} is an R package for estimating volatility of compounds. v2.1.0 incudes significant improvements in user interface🧑‍💻 , accuracy 🎯, and speed⏱️.

Blog post: https://datascience.cct.arizona.edu/news/2023/12/volcalc-v210-released-along-publication-frontiers-microbiology

Package website: https://meredith-lab.github.io/volcalc/

Frontiers in Microbiology paper: https://doi.org/10.3389/fmicb.2023.1267234

#Rstats #chemoinformatics #microbiology #VOCs

Any #SMARTS wizards out there? How would I write a SMARTS pattern for, say, an OH group and a chlorine attached anywhere to the same aromatic ring?

EDIT: I figured it out!
[OX2H][$(c1ccccc1Cl), $(c1ccc(cc1)Cl), $(c1cc(ccc1)Cl)]

#chemistry #chemoinformatics

my lightning talk from the #RDKitUGM2023 is now on YouTube - all about making your work that uses datasets derived from ChEMBL more reproducible

📺 Video: https://youtu.be/PY-xaoRoSOY?list=PLugOo5eIVY3ExzpyKll6GGz4FRgBD2qzN&t=28

📜 Slides: https://bit.ly/cth-rdkit-ugm-2023

🤖 Code/Docs: https://github.com/cthoyt/chembl-downloader

Get started with: pip install chembl-downloader

#cheminformatics #chemoinformatics #chembl #pubchem

my lightning talk from the #RDKitUGM2023 is now on YouTube - all about making your work that uses datasets derived from ChEMBL more reproducible

📺 Video: https://youtu.be/PY-xaoRoSOY?list=PLugOo5eIVY3ExzpyKll6GGz4FRgBD2qzN&t=28

📜 Slides: https://bit.ly/cth-rdkit-ugm-2023

🤖 Code/Docs: https://github.com/cthoyt/chembl-downloader

Get started with: pip install chembl-downloader

#cheminformatics #chemoinformatics #chembl #pubchem

my lightning talk from the #RDKitUGM2023 is now on YouTube - all about making your work that uses datasets derived from ChEMBL more reproducible

📺 Video: https://youtu.be/PY-xaoRoSOY?list=PLugOo5eIVY3ExzpyKll6GGz4FRgBD2qzN&t=28

📜 Slides: https://bit.ly/cth-rdkit-ugm-2023

🤖 Code/Docs: https://github.com/cthoyt/chembl-downloader

Get started with: pip install chembl-downloader

#cheminformatics #chemoinformatics #chembl #pubchem

my lightning talk from the #RDKitUGM2023 is now on YouTube - all about making your work that uses datasets derived from ChEMBL more reproducible

📺 Video: https://youtu.be/PY-xaoRoSOY?list=PLugOo5eIVY3ExzpyKll6GGz4FRgBD2qzN&t=28

📜 Slides: https://bit.ly/cth-rdkit-ugm-2023

🤖 Code/Docs: https://github.com/cthoyt/chembl-downloader

Get started with: pip install chembl-downloader

#cheminformatics #chemoinformatics #chembl #pubchem

my lightning talk from the #RDKitUGM2023 is now on YouTube - all about making your work that uses datasets derived from ChEMBL more reproducible

📺 Video: https://youtu.be/PY-xaoRoSOY?list=PLugOo5eIVY3ExzpyKll6GGz4FRgBD2qzN&t=28

📜 Slides: https://bit.ly/cth-rdkit-ugm-2023

🤖 Code/Docs: https://github.com/cthoyt/chembl-downloader

Get started with: pip install chembl-downloader

#cheminformatics #chemoinformatics #chembl #pubchem

If you're looking for resources to teach #machineLearning and some of its applications to #genomics or #chemoinformatics: I post most of my teaching materials on my website https://cazencott.info/index.php/pages/Teaching and they are available under a CC-BY license if you want to reuse them.

I consider it part of my job as a public servant to make what I create publicly available, but not everyone shares this take...

New blog post about my journey with the editors-in-chief of the Journal of Cheminformatics (@rguha and @[email protected]) to pilot a reproducibility review as part of submission.

https://cthoyt.com/2023/08/27/jcheminf-reproducibility-pilot.html

#cheminformatics #chemoinformatics #reproducibility #asapscience #chemistry #openscience #jcheminf #metascience

We’re excited to be starting the next phase of {volcalc} 📦 development in collaboration with Dr. Laura Meredith with funding from @RConsortium. {volcalc} is a WIP #rstats package for calculating estimated volatility of chemicals.

See our full announcement: https://datascience.cct.arizona.edu/news/2023/07/r-consortium-funds-volcalc-package-development

#chemoinformatics #chemistry #rstats

I spent some time today learning to read/write SMILES and SMARTS and although my brain hurts a bit, it's actually not *that* tough. SMARTS is like regular expressions, but for molecules. Like regex, it gets tricky when you need something very specific (e.g OH groups not on an aromatic ring; phenols but not nitrophenols). I wish there was a SMARTS equivalent of this interactive regex explorer: https://regex101.com/

#chemoinformatics #chemistry #regex

{webchem} 1.3.0 is released on CRAN! This version brings some new features to nist_ri() 🎉 and sadly deprecates some functions whose corresponding APIs no longer exist 💀. Read the full changelog here: https://docs.ropensci.org/webchem/news/index.html#webchem-130

@rOpenSci
#chemoinformatics #chemistry #rstats

🎉 Just got notice that we got funding from the R Consortium to work on a really interesting project! `volcalc` is an R package for calculating estimated volatility of chemicals. Currently only works for compounds in the KEGG database, but we're going to re-factor so it works on any SMILES, InChI, or .mol file representation. I'm super excited to work on this!

#chemoinformatics #chemistry #VOCs #volatiles #rstats

Try to use recent version exmol #exmol #rdkit #chemoinformatics https://iwatobipen.wordpress.com/2023/05/04/try-to-use-recent-version-exmol-exmol-rdkit-chemoinformatics/ via @iwatobipen

Hi everyone. I am a chemoinformatician who just jumped ship from Twitter. I hope we can recreate here what made Twitter so good sharing science. #introduction #chemoinformatics