@knimest.bsky.social
Code, not Drugs: The LLM Revolution in Computational Drug Design
open.substack.com/pub/medchema...
open.substack.com/pub/medchema...
Code, not Drugs: The LLM Revolution in Computational Drug Design
Process before product
open.substack.com
October 27, 2025 at 3:29 PM
Code, not Drugs: The LLM Revolution in Computational Drug Design
open.substack.com/pub/medchema...
open.substack.com/pub/medchema...
Reposted
An LLM-based chemical compound generator prompts some thoughts about what these might be good for:
The Latest in Automated Analog Generation
www.science.org
October 15, 2025 at 12:14 PM
An LLM-based chemical compound generator prompts some thoughts about what these might be good for:
Reposted
Never assume that you know all about what any drug molecule is doing in the body - where it's going, what it's binding to. A new example:
Rapamycin's Secrets
www.science.org
October 15, 2025 at 9:20 PM
Never assume that you know all about what any drug molecule is doing in the body - where it's going, what it's binding to. A new example:
Reposted
🔓Be sure to read this recent #OpenAccess work by Nils Metzler-Nolte & co: "Glycosidase-activated prodrugs of a cytotoxic iron chelator for targeted cancer therapy"👀
pubs.rsc.org/en/content/a...
📍@ruhr-uni-bochum.de 🧪
pubs.rsc.org/en/content/a...
📍@ruhr-uni-bochum.de 🧪
Glycosidase-activated prodrugs of a cytotoxic iron chelator for targeted cancer therapy
New glycoside-prodrugs based on the iron chelator deferasirox were designed. Selective enzymatic activation by glycosidases was observed within 24 hours, accompanied by cancer cell-selective…
pubs.rsc.org
August 29, 2025 at 8:35 AM
🔓Be sure to read this recent #OpenAccess work by Nils Metzler-Nolte & co: "Glycosidase-activated prodrugs of a cytotoxic iron chelator for targeted cancer therapy"👀
pubs.rsc.org/en/content/a...
📍@ruhr-uni-bochum.de 🧪
pubs.rsc.org/en/content/a...
📍@ruhr-uni-bochum.de 🧪
Reposted
🔓Read this #OpenAccess Review by @moorelab.bsky.social and colleagues which explores the historic and recent progress in the discovery of small molecule drugs for Ebola virus disease⬇️
pubs.rsc.org/en/content/articlelanding/2025/md/d5md00533g
📍University of Illinois Chicago 🧪
pubs.rsc.org/en/content/articlelanding/2025/md/d5md00533g
📍University of Illinois Chicago 🧪
Small molecule drug discovery for Ebola virus disease
Known for its widespread outbreaks, including the 2013–2016 epidemic that infected almost 29 000 individuals and resulted in approximately 11 300 deaths, Ebola virus (EBOV) and related filoviruses…
pubs.rsc.org
October 17, 2025 at 3:03 PM
🔓Read this #OpenAccess Review by @moorelab.bsky.social and colleagues which explores the historic and recent progress in the discovery of small molecule drugs for Ebola virus disease⬇️
pubs.rsc.org/en/content/articlelanding/2025/md/d5md00533g
📍University of Illinois Chicago 🧪
pubs.rsc.org/en/content/articlelanding/2025/md/d5md00533g
📍University of Illinois Chicago 🧪
Reposted
On the front cover of issue 10 is work by Yosuke Demizu and colleagues on analysing the linker rigidity and improve intracellular behaviour of three novel PROTACs targeting H-PGDS, read more here👇
pubs.rsc.org/en/content/a...
📍National Institute of Health Sciences, Kanagawa 🧪
pubs.rsc.org/en/content/a...
📍National Institute of Health Sciences, Kanagawa 🧪
October 16, 2025 at 9:02 AM
On the front cover of issue 10 is work by Yosuke Demizu and colleagues on analysing the linker rigidity and improve intracellular behaviour of three novel PROTACs targeting H-PGDS, read more here👇
pubs.rsc.org/en/content/a...
📍National Institute of Health Sciences, Kanagawa 🧪
pubs.rsc.org/en/content/a...
📍National Institute of Health Sciences, Kanagawa 🧪
Reposted
Earlier this year, a paper came out that suggested for many organic reactions stirring has little effect on reactions rates. Now, a group has released a preprint arguing that stirring remains critical for reproducibility, selectivity and scalability.
All stirred up: chemical engineers refute claims that ‘stirring doesn’t matter’
Failing to mix reactions in heterogeneous or industrial systems could cause numerous issues and might even be dangerous, preprint claims
www.chemistryworld.com
October 20, 2025 at 1:49 PM
Earlier this year, a paper came out that suggested for many organic reactions stirring has little effect on reactions rates. Now, a group has released a preprint arguing that stirring remains critical for reproducibility, selectivity and scalability.
Reposted
Finally out!
We have released a #medchem exercise (as a #KNIME workflow) in which you can apply isosteric replacement to a given scaffold and enumerate all the suggestions.
The files required to run it are available on wcair.dundee.ac.uk/training/tra... or hub.knime.com/s/n4K2My0xJX...
#chemsky
We have released a #medchem exercise (as a #KNIME workflow) in which you can apply isosteric replacement to a given scaffold and enumerate all the suggestions.
The files required to run it are available on wcair.dundee.ac.uk/training/tra... or hub.knime.com/s/n4K2My0xJX...
#chemsky
Data Management - WCAIR
Data management is an essential component of the drug discovery process. Without proper data management, it can be challenging to connect data across different disciplines, leading to missed informat...
wcair.dundee.ac.uk
February 3, 2025 at 1:19 PM
Finally out!
We have released a #medchem exercise (as a #KNIME workflow) in which you can apply isosteric replacement to a given scaffold and enumerate all the suggestions.
The files required to run it are available on wcair.dundee.ac.uk/training/tra... or hub.knime.com/s/n4K2My0xJX...
#chemsky
We have released a #medchem exercise (as a #KNIME workflow) in which you can apply isosteric replacement to a given scaffold and enumerate all the suggestions.
The files required to run it are available on wcair.dundee.ac.uk/training/tra... or hub.knime.com/s/n4K2My0xJX...
#chemsky
Reposted
Today, we’re spotlighting Ryushi Seo and his Just KNIME It! Season 3 data journey.
Just KNIME It! is the perfect way to build your KNIME skills — whether you're just starting or leveling up.
Season 4 of #JustKNIMEIt! starts this week, register 👉 knime.com/just-knime-i...
Just KNIME It! is the perfect way to build your KNIME skills — whether you're just starting or leveling up.
Season 4 of #JustKNIMEIt! starts this week, register 👉 knime.com/just-knime-i...
May 12, 2025 at 3:44 PM
Today, we’re spotlighting Ryushi Seo and his Just KNIME It! Season 3 data journey.
Just KNIME It! is the perfect way to build your KNIME skills — whether you're just starting or leveling up.
Season 4 of #JustKNIMEIt! starts this week, register 👉 knime.com/just-knime-i...
Just KNIME It! is the perfect way to build your KNIME skills — whether you're just starting or leveling up.
Season 4 of #JustKNIMEIt! starts this week, register 👉 knime.com/just-knime-i...
Reposted
v1.37.0 of the Vernalis #KNIME community contribution is now available for AP v5.4, with v5.3/v5.2 to follow. New PDB Connector features including #AlphaFold access in the Query executor, new Hit Count node, and the PDB SMILES Query node is retired - see forum.knime.com/t/vernalis-v... for details
Vernalis v1.37.0 Release - Changes to PDB Connector Nodes
We have just released v1.37.0 of our community plugin which brings in 1 new nodes, deprecates one node and adds new features to one existing node NEW Node - PDB Connector Hit Count This node does ex...
forum.knime.com
December 10, 2024 at 12:31 PM
v1.37.0 of the Vernalis #KNIME community contribution is now available for AP v5.4, with v5.3/v5.2 to follow. New PDB Connector features including #AlphaFold access in the Query executor, new Hit Count node, and the PDB SMILES Query node is retired - see forum.knime.com/t/vernalis-v... for details
Reposted
🚀 New to #cheminformatics? Check out #ChacMool — a set of #KNIME workflows by Carlos D. Ramírez Márquez & José L. Medina Franco that make #chemical #library analysis (descriptors, scaffolds, PAINS, fingerprints) easy & accessible! without coding! 🔬💻
📌 #READ → medium.com/low-code-for...
📌 #READ → medium.com/low-code-for...
Exploring Chemical Databases with KNIME
Low-code workflows for cheminformatics
medium.com
May 30, 2025 at 7:35 AM
🚀 New to #cheminformatics? Check out #ChacMool — a set of #KNIME workflows by Carlos D. Ramírez Márquez & José L. Medina Franco that make #chemical #library analysis (descriptors, scaffolds, PAINS, fingerprints) easy & accessible! without coding! 🔬💻
📌 #READ → medium.com/low-code-for...
📌 #READ → medium.com/low-code-for...
Reposted
🚀 Registration is open for the #Fribourg #WinterSchool in #DataAnalytics & #MachineLearning, Feb 2–13 2026.
📍Hybrid: at Fribourg University or online
🔍Topics: data analytics, predictive/causal machine learning, deep learning
💻 Software: Python, R, Julia, Knime
👉 Sign up: www.unifr.ch/appecon/en/w...
📍Hybrid: at Fribourg University or online
🔍Topics: data analytics, predictive/causal machine learning, deep learning
💻 Software: Python, R, Julia, Knime
👉 Sign up: www.unifr.ch/appecon/en/w...
September 1, 2025 at 10:44 AM
🚀 Registration is open for the #Fribourg #WinterSchool in #DataAnalytics & #MachineLearning, Feb 2–13 2026.
📍Hybrid: at Fribourg University or online
🔍Topics: data analytics, predictive/causal machine learning, deep learning
💻 Software: Python, R, Julia, Knime
👉 Sign up: www.unifr.ch/appecon/en/w...
📍Hybrid: at Fribourg University or online
🔍Topics: data analytics, predictive/causal machine learning, deep learning
💻 Software: Python, R, Julia, Knime
👉 Sign up: www.unifr.ch/appecon/en/w...
Reposted
Save the date! Next year's European #RDKit UGM will take place from 16-18 September in Darmstadt, Germany.
Pre-registration will open in early 2026.
Pre-registration will open in early 2026.
October 21, 2025 at 3:25 PM
Save the date! Next year's European #RDKit UGM will take place from 16-18 September in Darmstadt, Germany.
Pre-registration will open in early 2026.
Pre-registration will open in early 2026.
Reposted
If you are interested in more R graphics with knime I can offer this collection
medium.com/p/9241e033e4ac
medium.com/p/9241e033e4ac
Exploring the Power of R Graphics with KNIME: A Collection of Examples
Low-code data visualizations to enrich your data storytelling
medium.com
November 18, 2024 at 9:05 PM
If you are interested in more R graphics with knime I can offer this collection
medium.com/p/9241e033e4ac
medium.com/p/9241e033e4ac
Reposted
Great work @cedricgraebin.bsky.social ! Reminds me of the early workflows on myExperiment back in the early days of #KNIME (gulp! 12y ago 😬)
www.myexperiment.org/workflows/26...
www.myexperiment.org/workflows/26...
myExperiment - Workflows - RDKit-bioisosteres (sauberns) [KNIME Workflow]
www.myexperiment.org
November 27, 2024 at 4:53 AM
Great work @cedricgraebin.bsky.social ! Reminds me of the early workflows on myExperiment back in the early days of #KNIME (gulp! 12y ago 😬)
www.myexperiment.org/workflows/26...
www.myexperiment.org/workflows/26...
Reposted
diving deep on tools such as KNIME and its chemistry extensions - you can do some nice things with it, and we have been developing some tools with the platform as part of the free resources available at wcair.dundee.ac.uk/training/tra....
November 19, 2024 at 9:13 AM
diving deep on tools such as KNIME and its chemistry extensions - you can do some nice things with it, and we have been developing some tools with the platform as part of the free resources available at wcair.dundee.ac.uk/training/tra....
Reposted
Once more for the #knime #chemistry folks - I implemented the "fast" synchronous search for chemical structures in the PubChem database into a KNIME component.
hub.knime.com/s/bU6bz0lBve...
#chemsky
hub.knime.com/s/bU6bz0lBve...
#chemsky
PubChem Fast Structural Search – cgraebin001
This component implements the Fast synchronous search engine that is part of the PubChem Power User Gateway (PUG) REST API to search for molecules in the PubCh…
hub.knime.com
November 28, 2024 at 3:08 PM
Once more for the #knime #chemistry folks - I implemented the "fast" synchronous search for chemical structures in the PubChem database into a KNIME component.
hub.knime.com/s/bU6bz0lBve...
#chemsky
hub.knime.com/s/bU6bz0lBve...
#chemsky
Reposted
🔍 Webinar Highlights:
• Molecular descriptor calculations
• 3D coordinate generation
• Molecular fingerprinting techniques
• Structural pattern identification with SMARTS syntax
• Data analysis of calculated descriptors
• Seamless integration with KNIME and Python
• Molecular descriptor calculations
• 3D coordinate generation
• Molecular fingerprinting techniques
• Structural pattern identification with SMARTS syntax
• Data analysis of calculated descriptors
• Seamless integration with KNIME and Python
November 19, 2024 at 7:45 AM
🔍 Webinar Highlights:
• Molecular descriptor calculations
• 3D coordinate generation
• Molecular fingerprinting techniques
• Structural pattern identification with SMARTS syntax
• Data analysis of calculated descriptors
• Seamless integration with KNIME and Python
• Molecular descriptor calculations
• 3D coordinate generation
• Molecular fingerprinting techniques
• Structural pattern identification with SMARTS syntax
• Data analysis of calculated descriptors
• Seamless integration with KNIME and Python
Reposted
It would work the same way for KNIME or DataWarrior. KNIME can read XLSX files directly and can interpret structures submitted as SMILES, MOL, etc, if you add chemistry-enabled extensions (RDKit, Indigo, CDK). DataWarrior can import CSV files if I remember well.
p.s.: both are free and open-source
p.s.: both are free and open-source
October 22, 2024 at 8:39 AM
It would work the same way for KNIME or DataWarrior. KNIME can read XLSX files directly and can interpret structures submitted as SMILES, MOL, etc, if you add chemistry-enabled extensions (RDKit, Indigo, CDK). DataWarrior can import CSV files if I remember well.
p.s.: both are free and open-source
p.s.: both are free and open-source
Reposted
KNIME, the Konstanz Information Miner -- I had a lot of fun with this at University, and want to revisit at some point. It seemed like the most powerful tool nobody ever talks about.
November 10, 2023 at 2:00 AM
KNIME, the Konstanz Information Miner -- I had a lot of fun with this at University, and want to revisit at some point. It seemed like the most powerful tool nobody ever talks about.
Reposted
For the #knime #chemistry folks out there:
I am releasing some of the things I made for KNIME as standalone components. The first one is a refined, visualization-enabled ChEMBL chemical structure search. Hope it is useful! - hub.knime.com/cgraebin001/...
#ChemSky
I am releasing some of the things I made for KNIME as standalone components. The first one is a refined, visualization-enabled ChEMBL chemical structure search. Hope it is useful! - hub.knime.com/cgraebin001/...
#ChemSky
ChEMBL structure search – cgraebin001
This node takes a table with structures (either SDF/MOL, RDKit or SMILES format) and runs a structural search using the ChEMBL REST API web services. The searc…
hub.knime.com
November 22, 2024 at 12:00 PM
For the #knime #chemistry folks out there:
I am releasing some of the things I made for KNIME as standalone components. The first one is a refined, visualization-enabled ChEMBL chemical structure search. Hope it is useful! - hub.knime.com/cgraebin001/...
#ChemSky
I am releasing some of the things I made for KNIME as standalone components. The first one is a refined, visualization-enabled ChEMBL chemical structure search. Hope it is useful! - hub.knime.com/cgraebin001/...
#ChemSky
Reposted
One more for the #knime #chemistry folks around:
My last custom component for KNIME could find if a given chemical structure can be found on the #ChEMBL database. What about biological activities?
This second component retrieves does this using the ChEMBLID as query: hub.knime.com/s/22f3jdJjRK...
My last custom component for KNIME could find if a given chemical structure can be found on the #ChEMBL database. What about biological activities?
This second component retrieves does this using the ChEMBLID as query: hub.knime.com/s/22f3jdJjRK...
ChEMBL Activity Search by ID – cgraebin001
This component uses the ChEMBL REST webservices API to retrieve biological activities reported to a compound represented by its ChEMBLID. If you don't have the…
hub.knime.com
November 25, 2024 at 1:23 PM
One more for the #knime #chemistry folks around:
My last custom component for KNIME could find if a given chemical structure can be found on the #ChEMBL database. What about biological activities?
This second component retrieves does this using the ChEMBLID as query: hub.knime.com/s/22f3jdJjRK...
My last custom component for KNIME could find if a given chemical structure can be found on the #ChEMBL database. What about biological activities?
This second component retrieves does this using the ChEMBLID as query: hub.knime.com/s/22f3jdJjRK...
Reposted
All of that using an open-source software exploring the potential of a open-access database!
November 25, 2024 at 3:09 PM
All of that using an open-source software exploring the potential of a open-access database!
Reposted
Using the other #knime components I published, you can:
- from the chemical structure (SMILES), get the molecule ID
- from the molecule ID, get the biological activities reported for that compound and the document ID where they are
- from the document ID, get the reference!
- from the chemical structure (SMILES), get the molecule ID
- from the molecule ID, get the biological activities reported for that compound and the document ID where they are
- from the document ID, get the reference!
November 25, 2024 at 3:08 PM
Using the other #knime components I published, you can:
- from the chemical structure (SMILES), get the molecule ID
- from the molecule ID, get the biological activities reported for that compound and the document ID where they are
- from the document ID, get the reference!
- from the chemical structure (SMILES), get the molecule ID
- from the molecule ID, get the biological activities reported for that compound and the document ID where they are
- from the document ID, get the reference!
Reposted
Still on the #knime #chemistry topic: still exploring the #ChEMBL REST API, I made another component that can retrieve a document data (authors, journal title, year, volume, pages, DOI, PubMED ID, Patent ID) from the correspondent Document ChEMBLID
hub.knime.com/s/8a1Txmjb_R...
hub.knime.com/s/8a1Txmjb_R...
ChEMBL get Document by ID – cgraebin001
This component retrieves information about a document (Publication, Book, Patent, Dataset) in the ChEMBL using its identifier number (ChEMBLID) as query. Retri…
hub.knime.com
November 25, 2024 at 3:08 PM
Still on the #knime #chemistry topic: still exploring the #ChEMBL REST API, I made another component that can retrieve a document data (authors, journal title, year, volume, pages, DOI, PubMED ID, Patent ID) from the correspondent Document ChEMBLID
hub.knime.com/s/8a1Txmjb_R...
hub.knime.com/s/8a1Txmjb_R...