Axel Pahl
@apahl.bsky.social
Med. Chemist turned Data Scientist at Fraunhofer ITMP, Hamburg. Cell Painting. Linux enthusiast. Programming in Python & Rust (, Nim, Go, I just can't decide), general geek. Judo black belt.
Reposted by Axel Pahl
This week's #RDKit blog post shows how to create simple protein--ligand interaction diagrams.
I think there's potential to take this a bit further...
greglandrum.github.io/rdkit-blog/p...
I think there's potential to take this a bit further...
greglandrum.github.io/rdkit-blog/p...
Drawing simple protein–ligand interaction diagrams with the RDKit – RDKit blog
Quick, but useful
greglandrum.github.io
September 26, 2025 at 3:58 PM
This week's #RDKit blog post shows how to create simple protein--ligand interaction diagrams.
I think there's potential to take this a bit further...
greglandrum.github.io/rdkit-blog/p...
I think there's potential to take this a bit further...
greglandrum.github.io/rdkit-blog/p...
Reposted by Axel Pahl
“We only have a few minutes left so please keep your questions brief.”
“Thank you for your talk, before I ask my convoluted question and get to the point, please allow me to tell you my name, title, position, rank and academic biography…”
“Thank you for your talk, before I ask my convoluted question and get to the point, please allow me to tell you my name, title, position, rank and academic biography…”
September 17, 2025 at 8:11 AM
“We only have a few minutes left so please keep your questions brief.”
“Thank you for your talk, before I ask my convoluted question and get to the point, please allow me to tell you my name, title, position, rank and academic biography…”
“Thank you for your talk, before I ask my convoluted question and get to the point, please allow me to tell you my name, title, position, rank and academic biography…”
Reposted by Axel Pahl
Reposted by Axel Pahl
I will soon be posting a postdoc position in protein biochemistry/biophyics! Interested candidates are welcome to reach out at luclar@kemi.dtu.dk. Experience in protein expression, purification, and assay development is a must. Structural biology would be great! Please RT :)
May 24, 2025 at 8:25 AM
I will soon be posting a postdoc position in protein biochemistry/biophyics! Interested candidates are welcome to reach out at luclar@kemi.dtu.dk. Experience in protein expression, purification, and assay development is a must. Structural biology would be great! Please RT :)
Reposted by Axel Pahl
Rxn-INSIGHT also has some functions for molecules, but many more for reactions. Functional groups and rings are handled separately here:
github.com/mrodobbe/Rxn...
github.com/mrodobbe/Rxn...
March 8, 2025 at 1:58 PM
Rxn-INSIGHT also has some functions for molecules, but many more for reactions. Functional groups and rings are handled separately here:
github.com/mrodobbe/Rxn...
github.com/mrodobbe/Rxn...
Reposted by Axel Pahl
Reposted by Axel Pahl
I will be playing in the O2 Arena!
Well, I won't be playing, I'll be talking... and no, it's not the one in London but the one in Amsterdam...
But if you're around, it would be cool to meet you there. 😊
www.dtls.nl/data-represe...
Well, I won't be playing, I'll be talking... and no, it's not the one in London but the one in Amsterdam...
But if you're around, it would be cool to meet you there. 😊
www.dtls.nl/data-represe...
February 15, 2025 at 11:45 AM
I will be playing in the O2 Arena!
Well, I won't be playing, I'll be talking... and no, it's not the one in London but the one in Amsterdam...
But if you're around, it would be cool to meet you there. 😊
www.dtls.nl/data-represe...
Well, I won't be playing, I'll be talking... and no, it's not the one in London but the one in Amsterdam...
But if you're around, it would be cool to meet you there. 😊
www.dtls.nl/data-represe...
Reposted by Axel Pahl
If you work in drug discovery and you read one thing this weekend, make it this exceptional J Med Chem editorial. Hits on almost every blessed thing I’ve tweetorialized over the last several years.
Quantitation and Error Measurements in Dose–Response Curves
Quantitation and Error Measurements in Dose–Response Curves
Quantitation and Error Measurements in Dose–Response Curves
pubs.acs.org
January 31, 2025 at 6:30 PM
If you work in drug discovery and you read one thing this weekend, make it this exceptional J Med Chem editorial. Hits on almost every blessed thing I’ve tweetorialized over the last several years.
Quantitation and Error Measurements in Dose–Response Curves
Quantitation and Error Measurements in Dose–Response Curves
Reposted by Axel Pahl
Microsoft researchers introduce MatterGen, a model that can discover new materials tailored to specific needs—like efficient solar cells or CO2 recycling—advancing progress beyond trial-and-error experiments. www.microsoft.com/en-us/resear...
January 16, 2025 at 12:18 PM
Sunday morning, Hamburg Fischmarkt.
December 22, 2024 at 7:06 AM
Sunday morning, Hamburg Fischmarkt.
Reposted by Axel Pahl
Multiresistente Keime: Die Waffen gegen gefährliche Bakterien werden zunehmend stumpf, immer häufiger können lebensbedrohliche Infektionen nicht mehr therapiert werden. Ersatz gibt es bisher kaum. Im neuen Fraunhofer-Magazin stellen wir neue Chancen aus der angewandten Forschung vor: s.fhg.de/P3pj
December 9, 2024 at 11:32 AM
Multiresistente Keime: Die Waffen gegen gefährliche Bakterien werden zunehmend stumpf, immer häufiger können lebensbedrohliche Infektionen nicht mehr therapiert werden. Ersatz gibt es bisher kaum. Im neuen Fraunhofer-Magazin stellen wir neue Chancen aus der angewandten Forschung vor: s.fhg.de/P3pj
Reposted by Axel Pahl
Want to make beautiful scientific figures? Easy!
The NIH released a library of 2000+ free scientific illustrations called *BioArt*.
Check it out! bioart.niaid.nih.gov
#AcademicSky #PsychSciSky 🧠🟦 🧪
The NIH released a library of 2000+ free scientific illustrations called *BioArt*.
Check it out! bioart.niaid.nih.gov
#AcademicSky #PsychSciSky 🧠🟦 🧪
October 30, 2024 at 9:45 AM
Want to make beautiful scientific figures? Easy!
The NIH released a library of 2000+ free scientific illustrations called *BioArt*.
Check it out! bioart.niaid.nih.gov
#AcademicSky #PsychSciSky 🧠🟦 🧪
The NIH released a library of 2000+ free scientific illustrations called *BioArt*.
Check it out! bioart.niaid.nih.gov
#AcademicSky #PsychSciSky 🧠🟦 🧪
After almost 10 years on consecutive temporary contracts, it was time for me to leave the MPI in Dortmund. Thank you to everyone for the really good time.
November 3, 2024 at 12:52 PM
After almost 10 years on consecutive temporary contracts, it was time for me to leave the MPI in Dortmund. Thank you to everyone for the really good time.
Reposted by Axel Pahl
Fantastic resource for bio icons: NIH Bioart Source
Build figures, presentations, and illustrations with 2,000+ science and medical art visuals. This collection of high-quality, scientifically accurate vectors, #icons, and brushes is freely available within the public domain. bioart.niaid.nih.gov
Build figures, presentations, and illustrations with 2,000+ science and medical art visuals. This collection of high-quality, scientifically accurate vectors, #icons, and brushes is freely available within the public domain. bioart.niaid.nih.gov
October 29, 2024 at 7:19 AM
Fantastic resource for bio icons: NIH Bioart Source
Build figures, presentations, and illustrations with 2,000+ science and medical art visuals. This collection of high-quality, scientifically accurate vectors, #icons, and brushes is freely available within the public domain. bioart.niaid.nih.gov
Build figures, presentations, and illustrations with 2,000+ science and medical art visuals. This collection of high-quality, scientifically accurate vectors, #icons, and brushes is freely available within the public domain. bioart.niaid.nih.gov
Reposted by Axel Pahl
Reposted by Axel Pahl
Register! Broad Institute
Machine Learning for Drug Discovery
broad.io/mldd
Oct 31/Nov 1
In-person, or free virtual attendance!
Speakers:
Jennifer Listgarten
James Collins
Jakob Uszkoreit
Jian Tang Mila
Antonia Mey
Jakub Tomczak
Henry van den Bedem
Nicolas Stransky
Machine Learning for Drug Discovery
broad.io/mldd
Oct 31/Nov 1
In-person, or free virtual attendance!
Speakers:
Jennifer Listgarten
James Collins
Jakob Uszkoreit
Jian Tang Mila
Antonia Mey
Jakub Tomczak
Henry van den Bedem
Nicolas Stransky
Machine Learning in Drug Discovery Symposium
The 2024 Machine Learning in Drug Discovery Symposium will feature a half-day workshop on October 31, 2024 and a full day of talks on November 1, 2024. Learn more about the symposium and workshop on t...
broad.io
September 3, 2024 at 5:18 PM
Register! Broad Institute
Machine Learning for Drug Discovery
broad.io/mldd
Oct 31/Nov 1
In-person, or free virtual attendance!
Speakers:
Jennifer Listgarten
James Collins
Jakob Uszkoreit
Jian Tang Mila
Antonia Mey
Jakub Tomczak
Henry van den Bedem
Nicolas Stransky
Machine Learning for Drug Discovery
broad.io/mldd
Oct 31/Nov 1
In-person, or free virtual attendance!
Speakers:
Jennifer Listgarten
James Collins
Jakob Uszkoreit
Jian Tang Mila
Antonia Mey
Jakub Tomczak
Henry van den Bedem
Nicolas Stransky
Reposted by Axel Pahl
Hey friends! Just letting you know about the full hybrid conference "AI in Chemistry". In-person registration (Cambridge, UK) closes tonight, and virtual registration will be open a while longer. It's a *great* conference ⚗ www.rscbmcs.org/events/aiche...
7th AI in Chemistry - RSC BMCS
We organise international conferences that ensure the cross fertilisation of ideas amongst experts in our field
www.rscbmcs.org
September 2, 2024 at 8:29 AM
Hey friends! Just letting you know about the full hybrid conference "AI in Chemistry". In-person registration (Cambridge, UK) closes tonight, and virtual registration will be open a while longer. It's a *great* conference ⚗ www.rscbmcs.org/events/aiche...
Reposted by Axel Pahl
Join us and Herbert Waldmann, Dorothea Fiedler, Christian Hackenberger, Stephan Sieber, Tamir Gonen, Ralf Jungmann, Andrea Rentmeister, Ronald Micura, John Yates, Kerstin Goepfrich and Michael Jewett at the @GDChBiochem.bsky.social Conference (30.9.-02.10.24).
veranstaltungen.gdch.de/microsite/in...
veranstaltungen.gdch.de/microsite/in...
August 1, 2024 at 8:14 AM
Join us and Herbert Waldmann, Dorothea Fiedler, Christian Hackenberger, Stephan Sieber, Tamir Gonen, Ralf Jungmann, Andrea Rentmeister, Ronald Micura, John Yates, Kerstin Goepfrich and Michael Jewett at the @GDChBiochem.bsky.social Conference (30.9.-02.10.24).
veranstaltungen.gdch.de/microsite/in...
veranstaltungen.gdch.de/microsite/in...
LOL. This is really hilarious. And so close to the truth, it hurts.
github-roast.pages.dev
(via @denschub@schub.social)
github-roast.pages.dev
(via @denschub@schub.social)
GitHub Profile Roast 🔥🔥🔥
github-roast.pages.dev
August 5, 2024 at 6:07 PM
LOL. This is really hilarious. And so close to the truth, it hurts.
github-roast.pages.dev
(via @denschub@schub.social)
github-roast.pages.dev
(via @denschub@schub.social)
Cluster small molecules as Minimum Spanning Tree and visualize the results in an interactive, selectable scatter plot with structure tooltips: github.com/apahl/cluste...
July 18, 2024 at 10:04 AM
Cluster small molecules as Minimum Spanning Tree and visualize the results in an interactive, selectable scatter plot with structure tooltips: github.com/apahl/cluste...
Reposted by Axel Pahl
Please excuse a non-nature post. This is happening now to bring awareness to Long Covid. I've been watching for half an hour and already learned a lot. Dianna Cowern is an incredible science Youtuber who's been in bed with Long Covid for almost two years. Hosted by Simone Giertz & others. 🧪
Physics Girl LIVE with long Covid
Dianna is Live streaming a day in her life as someone suffering from long COVID and ME/CFS. The purpose of the Livestream is to raise money and awareness for...
www.youtube.com
July 6, 2024 at 4:47 PM
Please excuse a non-nature post. This is happening now to bring awareness to Long Covid. I've been watching for half an hour and already learned a lot. Dianna Cowern is an incredible science Youtuber who's been in bed with Long Covid for almost two years. Hosted by Simone Giertz & others. 🧪
We had discussed internally some time ago, that the fact, that all SELFIES encode for valid structures might be detrimental to machine learning. A Nature machine intelligence article now seems to confirm this:
www.nature.com/articles/s42...
#ChemInformatics
www.nature.com/articles/s42...
#ChemInformatics
Invalid SMILES are beneficial rather than detrimental to chemical language models - Nature Machine Intelligence
Generative models for chemical structures are often trained to create output in the common SMILES notation. Michael Skinnider shows that training models with the goal of avoiding the generation of inc...
www.nature.com
July 1, 2024 at 11:43 AM
We had discussed internally some time ago, that the fact, that all SELFIES encode for valid structures might be detrimental to machine learning. A Nature machine intelligence article now seems to confirm this:
www.nature.com/articles/s42...
#ChemInformatics
www.nature.com/articles/s42...
#ChemInformatics
Very interesting job opening at the MPI of Molecular Physiology in Dortmund in the field of data science on morphological cell imaging. This is the position for my succession at the COMAS:
www.mpi-dortmund.mpg.de/news/jobs/da...
#CellPainting #AcademicJobs
www.mpi-dortmund.mpg.de/news/jobs/da...
#CellPainting #AcademicJobs
Data Scientist
www.mpi-dortmund.mpg.de
June 19, 2024 at 8:32 AM
Very interesting job opening at the MPI of Molecular Physiology in Dortmund in the field of data science on morphological cell imaging. This is the position for my succession at the COMAS:
www.mpi-dortmund.mpg.de/news/jobs/da...
#CellPainting #AcademicJobs
www.mpi-dortmund.mpg.de/news/jobs/da...
#CellPainting #AcademicJobs
This is really driving me crazy: My boss does not want me to leave, I don't want to leave, but still I have to leave at the end of the year, because of the #WissenschaftsZeitvertragsGesetz. So today I reviewed the upcoming job posting for my successor, who should have exactly my qualifications.
May 8, 2024 at 3:14 PM
This is really driving me crazy: My boss does not want me to leave, I don't want to leave, but still I have to leave at the end of the year, because of the #WissenschaftsZeitvertragsGesetz. So today I reviewed the upcoming job posting for my successor, who should have exactly my qualifications.
Can you find activity in dark chemical matter? - Yes you can. With the #CellPainting assay.
pubs.acs.org/doi/10.1021/...
pubs.acs.org/doi/10.1021/...
May 2, 2024 at 6:15 AM
Can you find activity in dark chemical matter? - Yes you can. With the #CellPainting assay.
pubs.acs.org/doi/10.1021/...
pubs.acs.org/doi/10.1021/...