#cheminformatics — Public Fediverse posts

new blog post: "One Million IUPAC names #5: a new approach and 400k names" https://doi.org/10.59350/gqtbx-jta57 #openaccess #iupac #cheminformatics #blueObelisk

"Europe PMC, however, also provides the JATS XML files as download on their FTP site. Already that august 2025 I had a prototype and knew it would change the game. These gzipped XML files are about 150 to 250 MB. Unzipped, about 1 GB each."

Replies to this post show up in the blog.

Did you know that the Beilstein-Institut has always been a digital innovator in chemistry - from the Beilstein Database in the ‘80s to the digital infrastructure and standards in chemistry projects supported in the current Beilstein ChemInfo Labs 🧪💻?

➡️ https://www.beilstein-institut.de/en/projects/cheminfo-labs/?M=y

Join us in making chemical data accessible, findable, and reusable for everyone.

#BeilsteinChemInfoLabs #OpenScience #Cheminformatics #FAIRData #STRENDA #MIRAGE #Beilstein75

a macro to generate other macros was the best idea ever: now confirmed

(with the last version of emacs-indigo for pretty-much-memory-safe molecule manipulation inside emacs!)

https://github.com/gicrisf/emacs-indigo

#emacs #lisp #chemistry #cheminformatics #metaprogramming #programming #code #coding #fp

a macro to generate other macros was the best idea ever: now confirmed

(with the last version of emacs-indigo for pretty-much-memory-safe molecule manipulation inside emacs!)

https://github.com/gicrisf/emacs-indigo

#emacs #lisp #chemistry #cheminformatics #metaprogramming #programming #code #coding #fp

a macro to generate other macros was the best idea ever: now confirmed

(with the last version of emacs-indigo for pretty-much-memory-safe molecule manipulation inside emacs!)

https://github.com/gicrisf/emacs-indigo

#emacs #lisp #chemistry #cheminformatics #metaprogramming #programming #code #coding #fp

a macro to generate other macros was the best idea ever: now confirmed

(with the last version of emacs-indigo for pretty-much-memory-safe molecule manipulation inside emacs!)

https://github.com/gicrisf/emacs-indigo

#emacs #lisp #chemistry #cheminformatics #metaprogramming #programming #code #coding #fp

a macro to generate other macros was the best idea ever: now confirmed

(with the last version of emacs-indigo for pretty-much-memory-safe molecule manipulation inside emacs!)

https://github.com/gicrisf/emacs-indigo

#emacs #lisp #chemistry #cheminformatics #metaprogramming #programming #code #coding #fp

🧩 Could RNA and proteins share the same “shape language” for binding drugs?

🔗 Eigenvalue Ratios Reveal Shared Binding Pocket Shapes in RNA and Protein Structures. Computational and Structural Biotechnology Journal (CSBJ). DOI: https://doi.org/10.34133/csbj.0022

📚 CSBJ - A Science Partner Journal: https://spj.science.org/journal/csbj

#DrugDiscovery #StructuralBiology #ComputationalBiology #RNAResearch #ProteinScience #Bioinformatics #MolecularModeling #Genomics #Proteomics #Cheminformatics #LigandBinding

The Coordinated Action “Diagnostic, Therapeutic and Vaccine Viral Targets” of #ANRS MIE is organising a #webinar on #AI for molecular discovery. This webinar will explore how AI and #computational #modelling are advancing #drugdesign and protein research.
Speakers will present approaches for molecular design, prediction of protein variant effects and dynamics, and structural modelling of protein–protein interactions. The session will also take a critical perspective, addressing current limitations in #cheminformatics and practical considerations for researchers.

🚨 TOMORROW🚨
⚠️ AI for molecular discovery: From drug design to protein dynamics⚠️
April 15th 2026
12:30 - 14:00
Wednesday April 15th 2026, from 12:30 to 14:00 — online (Zoom)

Programme :

1️⃣ "AI for drug design" — Dragos Horvath, Strasbourg University
2️⃣ "Computational approaches for protein variant effect and motion prediction" — Elodie Laine, Sorbonne University
3️⃣ "Structural modelling and binding affinity prediction of the Human PDZ-PBM interactome" — Victor Reys, Utrecht University

➡️ Registration : https://services.hosting.augure.com/Response/c7juk/%7B6f9b7a92-f72c-4db8-9259-d92aaa0f0cc3%7D

#SWAT4HCLS is over.

Today, I am at the #KNCV CTC meeting, where we are launching the #Cheminformatics and #DrugDiscovery working group, as part of the CTC Section

OPSIN 2.9.0 has been released: https://chembl.blogspot.com/2026/03/opsin-v290-released.html

OPSIN is an IUPAC name parser that returns SMILES

"The release notes describe a mixture of minor bug fixes and improvements:"

#smiles #chemistry #iupac #cheminformatics #openscience

CDK 2.12 blogpost https://chem-bla-ics.linkedchemistry.info/2026/03/08/cdk-2.12.html https://doi.org/10.59350/gw9at-srp84

Replies will show up in the blog

#cdk #java #cheminformatics #openscience

The Coordinated Action “Diagnostic, Therapeutic and Vaccine Viral Targets” of #ANRS MIE is organising a #webinar on #AI for molecular discovery. This webinar will explore how AI and #computational #modelling are advancing #drugdesign and protein research.
Speakers will present approaches for molecular design, prediction of protein variant effects and dynamics, and structural modelling of protein–protein interactions. The session will also take a critical perspective, addressing current limitations in #cheminformatics and practical considerations for researchers.

🚨 MARK YOUR CALENDAR 🚨
⚠️ AI for molecular discovery: From drug design to protein dynamics⚠️
April 15th 2026
12:30 - 14:00
Wednesday April 15th 2026, from 12:30 to 14:00 — online (Zoom)

Programme :

1️⃣ "AI for drug design" — Dragos Horvath, Strasbourg University
2️⃣ "Computational approaches for protein variant effect and motion prediction" — Elodie Laine, Sorbonne University
3️⃣ "Structural modelling and binding affinity prediction of the Human PDZ-PBM interactome" — Victor Reys, Utrecht University

➡️ Registration : https://services.hosting.augure.com/Response/c7juk/%7B6f9b7a92-f72c-4db8-9259-d92aaa0f0cc3%7D

#OpenBabel is dead, long live #RDKit!

https://github.com/RMeli/spyrmsd/issues/149

On a more serius note, it would be cool to have a cheminformatics library that actually works. Don't get me wrong, RDKit is very cool - but you can feel all the underlying problems it has when using it.

#Cheminformatics

🤖 Can AI help us predict and prevent off-target effects in PROTAC drug design?

🔗 Predicting PROTAC off-target effects via warhead involvement levels in drug–target interactions using graph attention neural networks. Computational and Structural Biotechnology Journal, DOI: https://doi.org/10.1016/j.csbj.2025.10.028

📚 CSBJ: https://www.csbj.org/

#DrugDevelopment #StructuralBiology #ChemicalBiology #PROTAC #DrugDiscovery #Cheminformatics #Bioinformatics #PrecisionMedicine #TargetedProteinDegradation

✨ Is it time to rethink allosteric site prediction using internal protein nanoenvironments?

🔗 Protein allosteric site identification using machine learning and per amino acid residue reported internal protein nanoenvironment descriptors. Computational and Structural Biotechnology Journal, DOI: https://doi.org/10.1016/j.csbj.2024.10.036

📚 CSBJ: https://www.csbj.org/

#DrugDiscovery #ComputationalBiology #StructuralBiology #ProteinEngineering #Biophysics #Cheminformatics

excited to see @lipidmaps.bsky.social bridging to the #fediverse !

#lipidomics #ontology #cheminformatics

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

Fwd: "Unleashing 4 million IUPAC names into the wild" https://chembl.blogspot.com/2025/08/unleashing-4-million-iupac-names-into.html

"In support of Egon Willighagen's 'One Million IUPAC Names' project, we have just released more than 4 million IUPAC names text-mined from patents. Here are the details as listed on Zenodo:"

#cheminformatics #chemistry #iupac #openscience

ha, I managed to convert a CXSMILES in @wikidata via the MDL V2000 molfile and the #inchi webtool into an #InChI (!B) and InChIKey :) https://www.wikidata.org/wiki/Q66421202#P117

#cheminformatics #polymers

The outcomes of this workshop will directly shape the next phase of development, guiding the creation of a scientifically rigorous and user-focused search tool and Magres database (version 2), while also strengthening collaboration between CCP-NC, CCDC, and PSDI.

#PSDI #CCPNC #CCDC #Workshop #Database #Metadata #cheminformatics #Data #MaterialScience

The outcomes of this workshop will directly shape the next phase of development, guiding the creation of a scientifically rigorous and user-focused search tool and Magres database (version 2), while also strengthening collaboration between CCP-NC, CCDC, and PSDI.

#PSDI #CCPNC #CCDC #Workshop #Database #Metadata #cheminformatics #Data #MaterialScience

The outcomes of this workshop will directly shape the next phase of development, guiding the creation of a scientifically rigorous and user-focused search tool and Magres database (version 2), while also strengthening collaboration between CCP-NC, CCDC, and PSDI.

#PSDI #CCPNC #CCDC #Workshop #Database #Metadata #cheminformatics #Data #MaterialScience

Times are changing but order matters: Transferable prediction of small molecule liquid chromatography retention times
https://bio.informatik.uni-jena.de/2024/12/times-are-changing-but-order-matters/
#LCMS #RetentionTime #chromatograpy #bioinformatics #cheminformatics

interesting progress: "STOUT V2.0: SMILES to IUPAC name conversion using transformer models" https://doi.org/10.1186/s13321-024-00941-x

"The model was trained on a dataset of nearly 1 billion SMILES and corresponding IUPAC names, generated using OpenEye's Lexichem software. This new version achieves very high accuracy on test and benchmark datasets, demonstrating improved capability in producing longer IUPAC names with fewer errors overall."

#chemistry #cheminformatics #iupac

A really interesting preprint caught my attention from Connor Coley’s group at MIT. ShEPhERD diffusing shape, electrostatics, and pharmacophores for bioisosteric drug design https://macinchem.org/2024/11/23/shepherd-shape-electrostatics-and-pharmacophore-explicit-representation-diffusion/ #cheminformatics #RDKit

I had not see this #chemistry journal before: https://www.sciencedirect.com/journal/artificial-intelligence-chemistry That's a lot of #cheminformatics #chemometrics journals we have now. #elsevier

I had not see this #chemistry journal before: https://www.sciencedirect.com/journal/artificial-intelligence-chemistry That's a lot of #cheminformatics #chemometrics journals we have now. #elsevier

I had not see this #chemistry journal before: https://www.sciencedirect.com/journal/artificial-intelligence-chemistry That's a lot of #cheminformatics #chemometrics journals we have now. #elsevier

I had not see this #chemistry journal before: https://www.sciencedirect.com/journal/artificial-intelligence-chemistry That's a lot of #cheminformatics #chemometrics journals we have now. #elsevier

I had not see this #chemistry journal before: https://www.sciencedirect.com/journal/artificial-intelligence-chemistry That's a lot of #cheminformatics #chemometrics journals we have now. #elsevier

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

📝 "Small molecules in ChEMBL database"

👤 Jennifer HY Lin (@jhylin)

🔗 https://jhylin.github.io/Data_in_life_blog/posts/08_ML1-1_Small_molecules_in_ChEMBL_database/ML1-1_chembl_cpds.html

#pyladies #python #machinelearningprojects #scikitlearn #polars #jupyter #chembldatabase #cheminformatics

📝 "Small molecules in ChEMBL database"

👤 Jennifer HY Lin (@jhylin)

🔗 https://jhylin.github.io/Data_in_life_blog/posts/10_ML1-2_Small_molecules_in_ChEMBL_database/ML1-2_chembl_cpds.html

#pyladies #python #machinelearningprojects #scikitlearn #chembldatabase #cheminformatics

📝 "Small molecules in ChEMBL database"

👤 Jennifer HY Lin (@jhylin)

🔗 https://jhylin.github.io/Data_in_life_blog/posts/11_ML1-3_Small_molecules_in_ChEMBL_database/ML1-3_chembl_cpds.html

#pyladies #python #machinelearningprojects #scikitlearn #chembldatabase #cheminformatics

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

📝 "Working with scaffolds in small molecules"

👤 Jennifer HY Lin (@jhylin)

🔗 https://jhylin.github.io/Data_in_life_blog/posts/14_Scaffolds_in_small_molecules/chembl_anti-inf_data_prep_current.html

#pyladies #python #rdkit #datamol #pandas #polars #cheminformatics

📝 "Small molecules in ChEMBL database"

👤 Jennifer HY Lin (@jhylin)

🔗 https://jhylin.github.io/Data_in_life_blog/posts/10_ML2_Small_molecules_in_ChEMBL_database/ML2_chembl_cpds.html

#pyladies #python #machinelearningprojects #scikitlearn #chembldatabase #cheminformatics

📝 "Small molecules in ChEMBL database"

👤 Jennifer HY Lin (@jhylin)

🔗 https://jhylin.github.io/Data_in_life_blog/posts/11_ML3_Small_molecules_in_ChEMBL_database/ML3_chembl_cpds.html

#pyladies #python #machinelearningprojects #scikitlearn #chembldatabase #cheminformatics

date: 2023-04-03 12:20:46
by: Peter Kenny 🇹🇹🇬🇧🇧🇷🇺🇦🌻🇪🇺🇲🇦

#PhD opportunity: artificial intelligence approach to address drug #resistance in #infectious disease at University of Dundee (UK) closing 05-May-2023 #CompChem #cheminformatics #ChemPhD #AI #ML #infection #antibiotic #antibacterial #efflux https://www.dundee.ac.uk/phds/projects/ai-based-approach-address-drug-resistance-infectious-disease

🐦🔗: https://twitter.com/twitter/statuses/1642864718225321985
#PhdPosition

I'm making a tiny change to the Balsa #ebnf grammar to reject strings with terminating branches (e.g., "CCC(C)" and "CCC(C).O"). They should never be needed and just complicate canonicalization.

Working paper at: https://chemrxiv.org/engage/chemrxiv/article-details/632159bd173b5d04e2fc8b1a

#cheminformatics