Install roshambo2 to pixi env #memo #cheminformatics #RDKit
Recently I'm using pixi for environment managment. Because it works very fast and can handle not only conda but also pypi in local .pixi env. Today, I tried to install roshambo2 to pixi env. The original article is published from JCIM and…
Recently I'm using pixi for environment managment. Because it works very fast and can handle not only conda but also pypi in local .pixi env. Today, I tried to install roshambo2 to pixi env. The original article is published from JCIM and…
Install roshambo2 to pixi env #memo #cheminformatics #RDKit
Recently I'm using pixi for environment managment. Because it works very fast and can handle not only conda but also pypi in local .pixi env. Today, I tried to install roshambo2 to pixi env. The original article is published from JCIM and the code is available under MIT lisence.Article In this article arthors shows performance of ROSHAMBO2 on Gaming GPU.
iwatobipen.wordpress.com
November 9, 2025 at 7:25 AM
Install roshambo2 to pixi env #memo #cheminformatics #RDKit
Recently I'm using pixi for environment managment. Because it works very fast and can handle not only conda but also pypi in local .pixi env. Today, I tried to install roshambo2 to pixi env. The original article is published from JCIM and…
Recently I'm using pixi for environment managment. Because it works very fast and can handle not only conda but also pypi in local .pixi env. Today, I tried to install roshambo2 to pixi env. The original article is published from JCIM and…
This week's #RDKit blog post looks at LOBSTER, a nice molecular superposition data set that came out last year. Now that everything's loaded into a database using lwreg, I can start playing with the data in future posts.
greglandrum.github.io/rdkit-blog/p...
greglandrum.github.io/rdkit-blog/p...
Working with the LOBSTER Data set I – RDKit blog
Registering and working with a 3D data set using lwreg
greglandrum.github.io
November 8, 2025 at 4:38 PM
This week's #RDKit blog post looks at LOBSTER, a nice molecular superposition data set that came out last year. Now that everything's loaded into a database using lwreg, I can start playing with the data in future posts.
greglandrum.github.io/rdkit-blog/p...
greglandrum.github.io/rdkit-blog/p...
I know some people have had problems accessing the discord servers we use for the UGMs, so I'm trying an experiment with setting up a Zulip server for the #RDKit.
If this works well, we can leave it up as an informal chat/discussion point for the community.
rdkit.zulipchat.com/join/ay4ccup...
If this works well, we can leave it up as an informal chat/discussion point for the community.
rdkit.zulipchat.com/join/ay4ccup...
RDKit
Zulip organization for the RDKit community
rdkit.zulipchat.com
November 6, 2025 at 5:54 AM
I know some people have had problems accessing the discord servers we use for the UGMs, so I'm trying an experiment with setting up a Zulip server for the #RDKit.
If this works well, we can leave it up as an informal chat/discussion point for the community.
rdkit.zulipchat.com/join/ay4ccup...
If this works well, we can leave it up as an informal chat/discussion point for the community.
rdkit.zulipchat.com/join/ay4ccup...
Run MD simulation with Openff&Openmm on pixi’s env #cheminformatics #RDKit #pixi #memo
My background was organic chemistry but now I'm working as cheminformatitian. So I have lots of experiences of cheminformatics and medicinal chemistry but not many experiences of molecular simulation. But I'm…
My background was organic chemistry but now I'm working as cheminformatitian. So I have lots of experiences of cheminformatics and medicinal chemistry but not many experiences of molecular simulation. But I'm…
Run MD simulation with Openff&Openmm on pixi’s env #cheminformatics #RDKit #pixi #memo
My background was organic chemistry but now I'm working as cheminformatitian. So I have lots of experiences of cheminformatics and medicinal chemistry but not many experiences of molecular simulation. But I'm interested in the simulation field and openmm and openff are one of my favorite packages to learn MD. OpenMM and OpenFF are developed attractively and Jeff shared useful notebook at RDKit UGM 2024 and 2025.
iwatobipen.wordpress.com
November 2, 2025 at 7:08 AM
Run MD simulation with Openff&Openmm on pixi’s env #cheminformatics #RDKit #pixi #memo
My background was organic chemistry but now I'm working as cheminformatitian. So I have lots of experiences of cheminformatics and medicinal chemistry but not many experiences of molecular simulation. But I'm…
My background was organic chemistry but now I'm working as cheminformatitian. So I have lots of experiences of cheminformatics and medicinal chemistry but not many experiences of molecular simulation. But I'm…
to 1.9 for PostgreSQL version 13 and later. pg_cron is upgraded from 1.6.4 to 1.6.7 for PostgreSQL version 10 and later. postgis is upgraded from 3.5.2 to 3.6.0 for PostgreSQL version 13 and later. rdkit is upgraded from 4.6.1 to 4.7.0
October 30, 2025 at 10:35 PM
to 1.9 for PostgreSQL version 13 and later. pg_cron is upgraded from 1.6.4 to 1.6.7 for PostgreSQL version 10 and later. postgis is upgraded from 3.5.2 to 3.6.0 for PostgreSQL version 13 and later. rdkit is upgraded from 4.6.1 to 4.7.0
Origin
archlinux.org
October 28, 2025 at 1:40 PM
Writing code is a team sport. A community of collaborators. There are a lot of great communities out there: BioJava, CDK, BioPython, RDKit to name a few. They all learn from each other through the community process. "Iron sharpens iron", as the saying goes
October 24, 2025 at 7:27 AM
Writing code is a team sport. A community of collaborators. There are a lot of great communities out there: BioJava, CDK, BioPython, RDKit to name a few. They all learn from each other through the community process. "Iron sharpens iron", as the saying goes
This week I updated an older #RDKit blog post to show how to use the RDKit in your own C++ projects on Windows. That post now covers Linux, the Mac, and Windows.
greglandrum.github.io/rdkit-blog/p...
greglandrum.github.io/rdkit-blog/p...
Using the RDKit in a C++ program – RDKit blog
It’s actually pretty easy
greglandrum.github.io
October 23, 2025 at 1:25 PM
This week I updated an older #RDKit blog post to show how to use the RDKit in your own C++ projects on Windows. That post now covers Linux, the Mac, and Windows.
greglandrum.github.io/rdkit-blog/p...
greglandrum.github.io/rdkit-blog/p...
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.
Origin
archlinux.org
October 20, 2025 at 8:47 PM
Origin
archlinux.org
October 20, 2025 at 8:47 PM
Origin
archlinux.org
October 19, 2025 at 12:01 PM
The new #RDKit blog post shows off some reaction drawing tricks.
greglandrum.github.io/rdkit-blog/p...
greglandrum.github.io/rdkit-blog/p...
Displaying atom maps and highlighting with reactions – RDKit blog
How to display info about a reaction transformation on a set of specific reactants and products.
greglandrum.github.io
October 17, 2025 at 6:41 PM
The new #RDKit blog post shows off some reaction drawing tricks.
greglandrum.github.io/rdkit-blog/p...
greglandrum.github.io/rdkit-blog/p...
I mean, the worst part is that there are actual deterministic #openscience tools to do name => SMILES (or other chemical format) + depict in 2D. Combine OPSIN with RDKit.. maybe check PubChem or ChEMBL or other open database if people use an informal term.
Can generative AI be trusted to draw chemical structures? Not yet, according to two chemists who want to see the community take a tough stance against its use.
The chemistry community should ban drawing chemical structures with generative AI, chemists warn
AIs like Microsoft's Copilot, Google's Gemini and OpenAI's ChatGPT still make serious errors rendering structural formulae
www.chemistryworld.com
October 15, 2025 at 3:00 PM
I mean, the worst part is that there are actual deterministic #openscience tools to do name => SMILES (or other chemical format) + depict in 2D. Combine OPSIN with RDKit.. maybe check PubChem or ChEMBL or other open database if people use an informal term.
September's software push includes updates to- AlphaPulldown, Boltz, ChemEM, ColabDesign, cryoDRGN, EMReady2, GROMACS, HADDOCK, NMRFxAnalyst, NMRFxStructure, PowerFit, PyTom-Match-Pick, R, RDKit, RFDiffusion, Scipion, SSDraw, Starparser, Topaz, Volume_Seg_Tool, & Warp.
More here:
More here:
SBGrid Consortium - Software Updates
The SBGrid Consortium is an innovative global research computing group operated out of Harvard Medical School. SBGrid provides the global structural biology community with support for research…
buff.ly
October 8, 2025 at 4:04 PM
September's software push includes updates to- AlphaPulldown, Boltz, ChemEM, ColabDesign, cryoDRGN, EMReady2, GROMACS, HADDOCK, NMRFxAnalyst, NMRFxStructure, PowerFit, PyTom-Match-Pick, R, RDKit, RFDiffusion, Scipion, SSDraw, Starparser, Topaz, Volume_Seg_Tool, & Warp.
More here:
More here:
I forgot to post over the weekend...
The new #RDKit blog post is a short one showing how to get decent 2D renderings for systems with intramolecular hydrogen bonds.
greglandrum.github.io/rdkit-blog/p...
The new #RDKit blog post is a short one showing how to get decent 2D renderings for systems with intramolecular hydrogen bonds.
greglandrum.github.io/rdkit-blog/p...
Rendering intramolecular H bonds in 2D – RDKit blog
A simple approach to get nonbonded atoms close to each other.
greglandrum.github.io
October 6, 2025 at 3:53 AM
I forgot to post over the weekend...
The new #RDKit blog post is a short one showing how to get decent 2D renderings for systems with intramolecular hydrogen bonds.
greglandrum.github.io/rdkit-blog/p...
The new #RDKit blog post is a short one showing how to get decent 2D renderings for systems with intramolecular hydrogen bonds.
greglandrum.github.io/rdkit-blog/p...
Jan Jensen: Can you find hits by screening only 100 molecules?
YouTube video by RDKit
youtu.be
October 5, 2025 at 9:09 AM
GPU based fast Shape alignment of molecules #RDKit #Roshambo2 #Cheminformatics
Most of readers know that power of GPU change the way of cheminformatics. I introduced nvMolkit which is developed by NVIDIA for cheminformatics tasks. Now we can handle huge amount of data in short time 🙂 nvMolKit can…
Most of readers know that power of GPU change the way of cheminformatics. I introduced nvMolkit which is developed by NVIDIA for cheminformatics tasks. Now we can handle huge amount of data in short time 🙂 nvMolKit can…
GPU based fast Shape alignment of molecules #RDKit #Roshambo2 #Cheminformatics
Most of readers know that power of GPU change the way of cheminformatics. I introduced nvMolkit which is developed by NVIDIA for cheminformatics tasks. Now we can handle huge amount of data in short time 🙂 nvMolKit can calculate compound similarity and conformation rapidly with GPU but GPU assisted alignment is not implemented. Ligand based approach is common way of drug discovery evenif alpha fold3 is availabe in these days.
iwatobipen.wordpress.com
September 28, 2025 at 12:52 AM
GPU based fast Shape alignment of molecules #RDKit #Roshambo2 #Cheminformatics
Most of readers know that power of GPU change the way of cheminformatics. I introduced nvMolkit which is developed by NVIDIA for cheminformatics tasks. Now we can handle huge amount of data in short time 🙂 nvMolKit can…
Most of readers know that power of GPU change the way of cheminformatics. I introduced nvMolkit which is developed by NVIDIA for cheminformatics tasks. Now we can handle huge amount of data in short time 🙂 nvMolKit can…
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...
Our new paper now 🎉 Published: Cheminformatics Microservice V3!
Paper: doi.org/10.1186/s133...
🛠️ Web app + API: RDKit, CDK, Open Babel — NO install, 100% open-source.
Try now: app.naturalproducts.net
#Cheminformatics #OpenScience #Innovation #CompChem #Opensource
Paper: doi.org/10.1186/s133...
🛠️ Web app + API: RDKit, CDK, Open Babel — NO install, 100% open-source.
Try now: app.naturalproducts.net
#Cheminformatics #OpenScience #Innovation #CompChem #Opensource
Cheminformatics Microservices UI
Cheminformatics Microservices UI - A modern interface for chemical data analysis
app.naturalproducts.net
September 23, 2025 at 1:45 PM
Our new paper now 🎉 Published: Cheminformatics Microservice V3!
Paper: doi.org/10.1186/s133...
🛠️ Web app + API: RDKit, CDK, Open Babel — NO install, 100% open-source.
Try now: app.naturalproducts.net
#Cheminformatics #OpenScience #Innovation #CompChem #Opensource
Paper: doi.org/10.1186/s133...
🛠️ Web app + API: RDKit, CDK, Open Babel — NO install, 100% open-source.
Try now: app.naturalproducts.net
#Cheminformatics #OpenScience #Innovation #CompChem #Opensource
This week I updated an older #RDKit blog post that demonstrates how to set things up so that you can easily use the RDKit in your own C++ code.
greglandrum.github.io/rdkit-blog/p...
greglandrum.github.io/rdkit-blog/p...
Using the RDKit in a C++ program – RDKit blog
It’s actually pretty easy
greglandrum.github.io
September 20, 2025 at 2:45 AM
This week I updated an older #RDKit blog post that demonstrates how to set things up so that you can easily use the RDKit in your own C++ code.
greglandrum.github.io/rdkit-blog/p...
greglandrum.github.io/rdkit-blog/p...
Excited to announce a preprint describing our software package Meeko! Meeko is a Python package that uses RDKit for receptor and ligand preparation, including protonation, bond order, and connectivity and processing of docking results. It is customizable and suitable for high-throughput workflows.
September 18, 2025 at 12:37 AM
Excited to announce a preprint describing our software package Meeko! Meeko is a Python package that uses RDKit for receptor and ligand preparation, including protonation, bond order, and connectivity and processing of docking results. It is customizable and suitable for high-throughput workflows.
GitHub - NVIDIA-Digital-Bio/nvMolKit: A high-performance, GPU-accelerated library for key computational chemistry tasks, such as molecular similarity, conf... #nvidia #nvmolkit #molecularmodeling #compchem #morgan #fingerprints #tanimoto #mmff #rdkit #gpu #conformergeneration #minimization
September 16, 2025 at 5:55 AM
RDKit fingerprintかなり特異度が低いように見えるけど何か刺さるユースケースがあるのだろうか
September 16, 2025 at 4:40 AM
RDKit fingerprintかなり特異度が低いように見えるけど何か刺さるユースケースがあるのだろうか