#cheminformatics — Public Fediverse posts
Live and recent posts from across the Fediverse tagged #cheminformatics, aggregated by home.social.
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and hot on the heels, the CDK Scaffold extension had the 2.13 release too: https://doi.org/10.5281/zenodo.22000770
Based on CDK 2.13 and with some notes on how it handles stereochemistry and a fix. See https://github.com/cdk/cdk-scaffold/wiki/8.-Known-issues-with-stereochemistry-preservation#version-213 (and screenshot).
Full release notes here: https://github.com/cdk/cdk-scaffold/releases/tag/2.13
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and hot on the heels, the CDK Scaffold extension had the 2.13 release too: https://doi.org/10.5281/zenodo.22000770
Based on CDK 2.13 and with some notes on how it handles stereochemistry and a fix. See https://github.com/cdk/cdk-scaffold/wiki/8.-Known-issues-with-stereochemistry-preservation#version-213 (and screenshot).
Full release notes here: https://github.com/cdk/cdk-scaffold/releases/tag/2.13
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and hot on the heels, the CDK Scaffold extension had the 2.13 release too: https://doi.org/10.5281/zenodo.22000770
Based on CDK 2.13 and with some notes on how it handles stereochemistry and a fix. See https://github.com/cdk/cdk-scaffold/wiki/8.-Known-issues-with-stereochemistry-preservation#version-213 (and screenshot).
Full release notes here: https://github.com/cdk/cdk-scaffold/releases/tag/2.13
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and hot on the heels, the CDK Scaffold extension had the 2.13 release too: https://doi.org/10.5281/zenodo.22000770
Based on CDK 2.13 and with some notes on how it handles stereochemistry and a fix. See https://github.com/cdk/cdk-scaffold/wiki/8.-Known-issues-with-stereochemistry-preservation#version-213 (and screenshot).
Full release notes here: https://github.com/cdk/cdk-scaffold/releases/tag/2.13
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and hot on the heels, the CDK Scaffold extension had the 2.13 release too: https://doi.org/10.5281/zenodo.22000770
Based on CDK 2.13 and with some notes on how it handles stereochemistry and a fix. See https://github.com/cdk/cdk-scaffold/wiki/8.-Known-issues-with-stereochemistry-preservation#version-213 (and screenshot).
Full release notes here: https://github.com/cdk/cdk-scaffold/releases/tag/2.13
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CDK 2.13 was released: https://doi.org/10.5281/zenodo.21992083
- cdk-iordf now available separately
- more SMIRKS
- fragmenter for cicular substuctures
- reaction centers in MDL V2000
- CXSMILES coordinate bonds
- improved metal sandwich renderingFull release notes: https://github.com/cdk/cdk/releases/tag/cdk-2.13
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CDK 2.13 was released: https://doi.org/10.5281/zenodo.21992083
- cdk-iordf now available separately
- more SMIRKS
- fragmenter for cicular substuctures
- reaction centers in MDL V2000
- CXSMILES coordinate bonds
- improved metal sandwich renderingFull release notes: https://github.com/cdk/cdk/releases/tag/cdk-2.13
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CDK 2.13 was released: https://doi.org/10.5281/zenodo.21992083
- cdk-iordf now available separately
- more SMIRKS
- fragmenter for cicular substuctures
- reaction centers in MDL V2000
- CXSMILES coordinate bonds
- improved metal sandwich renderingFull release notes: https://github.com/cdk/cdk/releases/tag/cdk-2.13
-
CDK 2.13 was released: https://doi.org/10.5281/zenodo.21992083
- cdk-iordf now available separately
- more SMIRKS
- fragmenter for cicular substuctures
- reaction centers in MDL V2000
- CXSMILES coordinate bonds
- improved metal sandwich renderingFull release notes: https://github.com/cdk/cdk/releases/tag/cdk-2.13
-
CDK 2.13 was released: https://doi.org/10.5281/zenodo.21992083
- cdk-iordf now available separately
- more SMIRKS
- fragmenter for cicular substuctures
- reaction centers in MDL V2000
- CXSMILES coordinate bonds
- improved metal sandwich renderingFull release notes: https://github.com/cdk/cdk/releases/tag/cdk-2.13
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RE: https://fosstodon.org/@zotero/117112205045153094
" ... and “h2o” will find “H<sub>2</sub>O” and “H₂O”, and vice versa."
But will it do that too when I search for "XLYOFNOQVPJJNP-UHFFFAOYSA-N" ?
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RE: https://fosstodon.org/@zotero/117112205045153094
" ... and “h2o” will find “H<sub>2</sub>O” and “H₂O”, and vice versa."
But will it do that too when I search for "XLYOFNOQVPJJNP-UHFFFAOYSA-N" ?
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RE: https://fosstodon.org/@zotero/117112205045153094
" ... and “h2o” will find “H<sub>2</sub>O” and “H₂O”, and vice versa."
But will it do that too when I search for "XLYOFNOQVPJJNP-UHFFFAOYSA-N" ?
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RE: https://fosstodon.org/@zotero/117112205045153094
" ... and “h2o” will find “H<sub>2</sub>O” and “H₂O”, and vice versa."
But will it do that too when I search for "XLYOFNOQVPJJNP-UHFFFAOYSA-N" ?
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RE: https://fosstodon.org/@zotero/117112205045153094
" ... and “h2o” will find “H<sub>2</sub>O” and “H₂O”, and vice versa."
But will it do that too when I search for "XLYOFNOQVPJJNP-UHFFFAOYSA-N" ?
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Computational Biologist - Fully Remote
micro1Computational Biologists (MSc or PhD) needed for fully remote contract work (up to $120/hour!). Ideally looking for experience in medicinal chemistry
See the full job description on jobRxiv: https://jobrxiv.org/job/micro1-27778-computational-biologist-fully-remote/
#bioinformatics #cheminformatics #computationalbiology #drugdiscovery #medicinalchemistry #S...
https://jobrxiv.org/job/micro1-27778-computational-biologist-fully-remote/?fsp_sid=14384 -
Computational Biologist - Fully Remote
micro1Computational Biologists (MSc or PhD) needed for fully remote contract work (up to $120/hour!). Ideally looking for experience in medicinal chemistry
See the full job description on jobRxiv: https://jobrxiv.org/job/micro1-27778-computational-biologist-fully-remote/
#bioinformatics #cheminformatics #computationalbiology #drugdiscovery #medicinalchemistry #S...
https://jobrxiv.org/job/micro1-27778-computational-biologist-fully-remote/?fsp_sid=14384 -
Computational Biologist - Fully Remote
micro1Computational Biologists (MSc or PhD) needed for fully remote contract work (up to $120/hour!). Ideally looking for experience in medicinal chemistry
See the full job description on jobRxiv: https://jobrxiv.org/job/micro1-27778-computational-biologist-fully-remote/
#bioinformatics #cheminformatics #computationalbiology #drugdiscovery #medicinalchemistry #S...
https://jobrxiv.org/job/micro1-27778-computational-biologist-fully-remote/?fsp_sid=14384 -
Computational Biologist - Fully Remote
micro1Computational Biologists (MSc or PhD) needed for fully remote contract work (up to $120/hour!). Ideally looking for experience in medicinal chemistry
See the full job description on jobRxiv: https://jobrxiv.org/job/micro1-27778-computational-biologist-fully-remote/
#bioinformatics #cheminformatics #computationalbiology #drugdiscovery #medicinalchemistry #S...
https://jobrxiv.org/job/micro1-27778-computational-biologist-fully-remote/?fsp_sid=14384 -
Computational Biologist - Fully Remote
micro1Computational Biologists (MSc or PhD) needed for fully remote contract work (up to $120/hour!). Ideally looking for experience in medicinal chemistry
See the full job description on jobRxiv: https://jobrxiv.org/job/micro1-27778-computational-biologist-fully-remote/
#bioinformatics #cheminformatics #computationalbiology #drugdiscovery #medicinalchemistry #S...
https://jobrxiv.org/job/micro1-27778-computational-biologist-fully-remote/?fsp_sid=14384 -
happy that I can now follow the InChI Trust posts here on #mastodon too now! @inchi-trust.bsky.social
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happy that I can now follow the InChI Trust posts here on #mastodon too now! @inchi-trust.bsky.social
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happy that I can now follow the InChI Trust posts here on #mastodon too now! @inchi-trust.bsky.social
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happy that I can now follow the InChI Trust posts here on #mastodon too now! @inchi-trust.bsky.social
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happy that I can now follow the InChI Trust posts here on #mastodon too now! @inchi-trust.bsky.social
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I have an opening in my group at RWTH Aachen University for a research internship for a bachelor or master's student in chemistry or computer science who would like to learn about cheminformatics methods in catalyst design for plastics recycling. Most appropriate for someone already based in Bonn or Aachen
more info: https://zenodo.org/records/20758266
#cheminformatics #circulareconomy #recycling #chemistry #internship #informatics #inorganic
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I have an opening in my group at RWTH Aachen University for a research internship for a bachelor or master's student in chemistry or computer science who would like to learn about cheminformatics methods in catalyst design for plastics recycling. Most appropriate for someone already based in Bonn or Aachen
more info: https://zenodo.org/records/20758266
#cheminformatics #circulareconomy #recycling #chemistry #internship #informatics #inorganic
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I have an opening in my group at RWTH Aachen University for a research internship for a bachelor or master's student in chemistry or computer science who would like to learn about cheminformatics methods in catalyst design for plastics recycling. Most appropriate for someone already based in Bonn or Aachen
more info: https://zenodo.org/records/20758266
#cheminformatics #circulareconomy #recycling #chemistry #internship #informatics #inorganic
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I have an opening in my group at RWTH Aachen University for a research internship for a bachelor or master's student in chemistry or computer science who would like to learn about cheminformatics methods in catalyst design for plastics recycling. Most appropriate for someone already based in Bonn or Aachen
more info: https://zenodo.org/records/20758266
#cheminformatics #circulareconomy #recycling #chemistry #internship #informatics #inorganic
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new blog: "Molecular Inorganics: SMILES, MDL molfile v3000, and InChIs" https://doi.org/10.59350/yhf27-fp921
"Both use the SMILES, but not all SMILES captures all the chemistry we need. And the InChI software needs an V3000 MDL Molfile. Thanks to John and other @cdk developers, there is good support for recent cheminformatics software, but I was not sure it had what I would need."
Replies to this post show up in the blog.
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new blog: "Molecular Inorganics: SMILES, MDL molfile v3000, and InChIs" https://doi.org/10.59350/yhf27-fp921
"Both use the SMILES, but not all SMILES captures all the chemistry we need. And the InChI software needs an V3000 MDL Molfile. Thanks to John and other @cdk developers, there is good support for recent cheminformatics software, but I was not sure it had what I would need."
Replies to this post show up in the blog.
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new blog: "Molecular Inorganics: SMILES, MDL molfile v3000, and InChIs" https://doi.org/10.59350/yhf27-fp921
"Both use the SMILES, but not all SMILES captures all the chemistry we need. And the InChI software needs an V3000 MDL Molfile. Thanks to John and other @cdk developers, there is good support for recent cheminformatics software, but I was not sure it had what I would need."
Replies to this post show up in the blog.
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new blog: "Molecular Inorganics: SMILES, MDL molfile v3000, and InChIs" https://doi.org/10.59350/yhf27-fp921
"Both use the SMILES, but not all SMILES captures all the chemistry we need. And the InChI software needs an V3000 MDL Molfile. Thanks to John and other @cdk developers, there is good support for recent cheminformatics software, but I was not sure it had what I would need."
Replies to this post show up in the blog.
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new blog: "Molecular Inorganics: SMILES, MDL molfile v3000, and InChIs" https://doi.org/10.59350/yhf27-fp921
"Both use the SMILES, but not all SMILES captures all the chemistry we need. And the InChI software needs an V3000 MDL Molfile. Thanks to John and other @cdk developers, there is good support for recent cheminformatics software, but I was not sure it had what I would need."
Replies to this post show up in the blog.
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I can do the same thing for polymers (here excluding the biopolymers): https://qlever.dev/wikidata/okph2M?exec=true
Again, with links to @Wikipedia and here, of course, using CXSMILES as preferred represenation
The question is, can this be used as input to create InChIs for these organometalics and polymers?
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I can do the same thing for polymers (here excluding the biopolymers): https://qlever.dev/wikidata/okph2M?exec=true
Again, with links to @Wikipedia and here, of course, using CXSMILES as preferred represenation
The question is, can this be used as input to create InChIs for these organometalics and polymers?
-
I can do the same thing for polymers (here excluding the biopolymers): https://qlever.dev/wikidata/okph2M?exec=true
Again, with links to @Wikipedia and here, of course, using CXSMILES as preferred represenation
The question is, can this be used as input to create InChIs for these organometalics and polymers?
-
I can do the same thing for polymers (here excluding the biopolymers): https://qlever.dev/wikidata/okph2M?exec=true
Again, with links to @Wikipedia and here, of course, using CXSMILES as preferred represenation
The question is, can this be used as input to create InChIs for these organometalics and polymers?
-
I can do the same thing for polymers (here excluding the biopolymers): https://qlever.dev/wikidata/okph2M?exec=true
Again, with links to @Wikipedia and here, of course, using CXSMILES as preferred represenation
The question is, can this be used as input to create InChIs for these organometalics and polymers?
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I am at a technical InChI meeting, discussing about wonderful chemistry, such as organometalics. I am finding currently multiple organometalic compounds in @wikidata and @wikipedia: https://w.wiki/SgFB
What is your favorite organometalic compound in Wikipedia?
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I am at a technical InChI meeting, discussing about wonderful chemistry, such as organometalics. I am finding currently multiple organometalic compounds in @wikidata and @wikipedia: https://w.wiki/SgFB
What is your favorite organometalic compound in Wikipedia?
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I am at a technical InChI meeting, discussing about wonderful chemistry, such as organometalics. I am finding currently multiple organometalic compounds in @wikidata and @wikipedia: https://w.wiki/SgFB
What is your favorite organometalic compound in Wikipedia?
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I am at a technical InChI meeting, discussing about wonderful chemistry, such as organometalics. I am finding currently multiple organometalic compounds in @wikidata and @wikipedia: https://w.wiki/SgFB
What is your favorite organometalic compound in Wikipedia?
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I am at a technical InChI meeting, discussing about wonderful chemistry, such as organometalics. I am finding currently multiple organometalic compounds in @wikidata and @wikipedia: https://w.wiki/SgFB
What is your favorite organometalic compound in Wikipedia?
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Extended-Connectivity Fingerprints in APL
Post: https://butwhyisthat.substack.com/p/ecfp
Code: https://github.com/manas02/ecfp -
Extended-Connectivity Fingerprints in APL
Post: https://butwhyisthat.substack.com/p/ecfp
Code: https://github.com/manas02/ecfp -
Our fingerprint analysis work has now been published 🎉 --> link.springer.com/article/10.1... Also check out our small helper library #chemap --> github.com/matchms/chemap (work together with @julianpollmann.bsky.social) #cheminformatics #openscience #Python
Count your bits: fingerprint b... -
A newly developed evaluative framework that tests the reliability, transparency, and chemical reasoning of artificial intelligence (AI) models used in the development of new antibiotics.
#Cheminformatics #ComputationalBiology #Pharmacology #Microbiology #ArtificialIntelligence #sflorg
https://www.sflorg.com/2026/06/cobi06262601.html -
A newly developed evaluative framework that tests the reliability, transparency, and chemical reasoning of artificial intelligence (AI) models used in the development of new antibiotics.
#Cheminformatics #ComputationalBiology #Pharmacology #Microbiology #ArtificialIntelligence #sflorg
https://www.sflorg.com/2026/06/cobi06262601.html -
A newly developed evaluative framework that tests the reliability, transparency, and chemical reasoning of artificial intelligence (AI) models used in the development of new antibiotics.
#Cheminformatics #ComputationalBiology #Pharmacology #Microbiology #ArtificialIntelligence #sflorg
https://www.sflorg.com/2026/06/cobi06262601.html -
A newly developed evaluative framework that tests the reliability, transparency, and chemical reasoning of artificial intelligence (AI) models used in the development of new antibiotics.
#Cheminformatics #ComputationalBiology #Pharmacology #Microbiology #ArtificialIntelligence #sflorg
https://www.sflorg.com/2026/06/cobi06262601.html -
A newly developed evaluative framework that tests the reliability, transparency, and chemical reasoning of artificial intelligence (AI) models used in the development of new antibiotics.
#Cheminformatics #ComputationalBiology #Pharmacology #Microbiology #ArtificialIntelligence #sflorg
https://www.sflorg.com/2026/06/cobi06262601.html -
ИИ в химии: история участия в хакатоне и рефлексия после
Всем привет! Меня зовут Константин Ушенин, я — ведущий научный сотрудник в AIRI, занимаюсь приложениями искусственного интеллекта в химии и фармакологии. В конце марта 2026 года мы с коллегами выиграли суточный хакатон от Сбера, ИТМО и СПБ ГБУ Молодёжного пространства «ПРОСТО» по созданию ИИ‑ассистента для планирования синтеза в лаборатории органической химии. Мероприятие прошло три месяца назад, однако мы завершили рефлексию результата только сейчас и решили сделать полный разбор. В этом посте вы узнаете про этапы нашей подготовки, выработку победной стратегии, решение проблем, возникавших по ходу соревнований, и наш подход к подготовке финальной презентации. В конце проведен анализ наших правильных и неправильных решений, а также дана оценка того, как реальное продуктовое решение должно отличаться от созданного на хакатоне. Но технологический ИИ‑стек на службе у химии — это не самое главное, о чём я хотел бы рассказать. Ключевую роль в нашей победе сыграла организация команды, распределение ролей и стрессоустойчивость всех её членов. Путь к первому месту оказался полным разных испытаний: начиная от неудобного стола и заканчивая хакерской атакой на наше решение за полчаса до защиты. В общем, получилось довольно остросюжетно, приятного чтения!
https://habr.com/ru/companies/airi/articles/1050580/
#hackaton #agentic_ai #chemistry #cheminformatics #llmагент #агентный_ии #хакатон
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ИИ в химии: история участия в хакатоне и рефлексия после
Всем привет! Меня зовут Константин Ушенин, я — ведущий научный сотрудник в AIRI, занимаюсь приложениями искусственного интеллекта в химии и фармакологии. В конце марта 2026 года мы с коллегами выиграли суточный хакатон от Сбера, ИТМО и СПБ ГБУ Молодёжного пространства «ПРОСТО» по созданию ИИ‑ассистента для планирования синтеза в лаборатории органической химии. Мероприятие прошло три месяца назад, однако мы завершили рефлексию результата только сейчас и решили сделать полный разбор. В этом посте вы узнаете про этапы нашей подготовки, выработку победной стратегии, решение проблем, возникавших по ходу соревнований, и наш подход к подготовке финальной презентации. В конце проведен анализ наших правильных и неправильных решений, а также дана оценка того, как реальное продуктовое решение должно отличаться от созданного на хакатоне. Но технологический ИИ‑стек на службе у химии — это не самое главное, о чём я хотел бы рассказать. Ключевую роль в нашей победе сыграла организация команды, распределение ролей и стрессоустойчивость всех её членов. Путь к первому месту оказался полным разных испытаний: начиная от неудобного стола и заканчивая хакерской атакой на наше решение за полчаса до защиты. В общем, получилось довольно остросюжетно, приятного чтения!
https://habr.com/ru/companies/airi/articles/1050580/
#hackaton #agentic_ai #chemistry #cheminformatics #llmагент #агентный_ии #хакатон
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ИИ в химии: история участия в хакатоне и рефлексия после
Всем привет! Меня зовут Константин Ушенин, я — ведущий научный сотрудник в AIRI, занимаюсь приложениями искусственного интеллекта в химии и фармакологии. В конце марта 2026 года мы с коллегами выиграли суточный хакатон от Сбера, ИТМО и СПБ ГБУ Молодёжного пространства «ПРОСТО» по созданию ИИ‑ассистента для планирования синтеза в лаборатории органической химии. Мероприятие прошло три месяца назад, однако мы завершили рефлексию результата только сейчас и решили сделать полный разбор. В этом посте вы узнаете про этапы нашей подготовки, выработку победной стратегии, решение проблем, возникавших по ходу соревнований, и наш подход к подготовке финальной презентации. В конце проведен анализ наших правильных и неправильных решений, а также дана оценка того, как реальное продуктовое решение должно отличаться от созданного на хакатоне. Но технологический ИИ‑стек на службе у химии — это не самое главное, о чём я хотел бы рассказать. Ключевую роль в нашей победе сыграла организация команды, распределение ролей и стрессоустойчивость всех её членов. Путь к первому месту оказался полным разных испытаний: начиная от неудобного стола и заканчивая хакерской атакой на наше решение за полчаса до защиты. В общем, получилось довольно остросюжетно, приятного чтения!
https://habr.com/ru/companies/airi/articles/1050580/
#hackaton #agentic_ai #chemistry #cheminformatics #llmагент #агентный_ии #хакатон
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While playing around a bit more with @marimo_io's #molab, although I was able to make #RDKit work, it seems py3Dmol (https://pypi.org/project/py3Dmol/) does not work as it's supposed to (i.e. I can't get 3D molecules to display in the notebook). I likely may have missed other stuff that needs to be imported, so: has anyone else tried this combination and made it work?
(Otherwise, alternatives for making 3D molecules show up in molab are welcome!)
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While playing around a bit more with @marimo_io's #molab, although I was able to make #RDKit work, it seems py3Dmol (https://pypi.org/project/py3Dmol/) does not work as it's supposed to (i.e. I can't get 3D molecules to display in the notebook). I likely may have missed other stuff that needs to be imported, so: has anyone else tried this combination and made it work?
(Otherwise, alternatives for making 3D molecules show up in molab are welcome!)
-
While playing around a bit more with @marimo_io's #molab, although I was able to make #RDKit work, it seems py3Dmol (https://pypi.org/project/py3Dmol/) does not work as it's supposed to (i.e. I can't get 3D molecules to display in the notebook). I likely may have missed other stuff that needs to be imported, so: has anyone else tried this combination and made it work?
(Otherwise, alternatives for making 3D molecules show up in molab are welcome!)
-
While playing around a bit more with @marimo_io's #molab, although I was able to make #RDKit work, it seems py3Dmol (https://pypi.org/project/py3Dmol/) does not work as it's supposed to (i.e. I can't get 3D molecules to display in the notebook). I likely may have missed other stuff that needs to be imported, so: has anyone else tried this combination and made it work?
(Otherwise, alternatives for making 3D molecules show up in molab are welcome!)
-
While playing around a bit more with @marimo_io's #molab, although I was able to make #RDKit work, it seems py3Dmol (https://pypi.org/project/py3Dmol/) does not work as it's supposed to (i.e. I can't get 3D molecules to display in the notebook). I likely may have missed other stuff that needs to be imported, so: has anyone else tried this combination and made it work?
(Otherwise, alternatives for making 3D molecules show up in molab are welcome!)