pen(Taka)
@iwatobipen.bsky.social
Medicinal Chemist, Cheminformatician, Runner and ?
ourworldindata.org/brief-histor...
Worth to read!
Worth to read!
The brief history of artificial intelligence: the world has changed fast — what might be next?
Little is as important for the world’s future and our own lives as how this history continues.
ourworldindata.org
November 24, 2025 at 2:51 AM
ourworldindata.org/brief-histor...
Worth to read!
Worth to read!
Similarity screening with RDKit #RDKit #SimilarityScreener #memo #cheminformatics
Similarity based screening is one of the common way to explore SAR rapidly. For example if you got hit compound but lack of human resources for making analogue compounds, catalogue SAR is useful way to expand SAR. Of…
Similarity based screening is one of the common way to explore SAR rapidly. For example if you got hit compound but lack of human resources for making analogue compounds, catalogue SAR is useful way to expand SAR. Of…
Similarity screening with RDKit #RDKit #SimilarityScreener #memo #cheminformatics
Similarity based screening is one of the common way to explore SAR rapidly. For example if you got hit compound but lack of human resources for making analogue compounds, catalogue SAR is useful way to expand SAR. Of course 'SIMILARITY' is really difficut term in cheminfomratics. There are lots of metrics for measuring compound similarity. I will not describe the topic in this post 🙂
iwatobipen.wordpress.com
November 23, 2025 at 6:23 AM
Similarity screening with RDKit #RDKit #SimilarityScreener #memo #cheminformatics
Similarity based screening is one of the common way to explore SAR rapidly. For example if you got hit compound but lack of human resources for making analogue compounds, catalogue SAR is useful way to expand SAR. Of…
Similarity based screening is one of the common way to explore SAR rapidly. For example if you got hit compound but lack of human resources for making analogue compounds, catalogue SAR is useful way to expand SAR. Of…
Reposted by pen(Taka)
This week's #RDKit blog post continues my look at the LOBSTER data set. This one got a bit derailed because I found a bug while working on it.
greglandrum.github.io/rdkit-blog/p...
greglandrum.github.io/rdkit-blog/p...
Working with the LOBSTER Data set II – RDKit blog
Conformer generation and comparing 3D fingerprints
greglandrum.github.io
November 17, 2025 at 5:47 AM
This week's #RDKit blog post continues my look at the LOBSTER data set. This one got a bit derailed because I found a bug while working on it.
greglandrum.github.io/rdkit-blog/p...
greglandrum.github.io/rdkit-blog/p...
I tried to install Openforld3 to my personal computer with pixi. It succeeded. I canceld the process because size of parameters were too big. So I will try again on HPC env tomorrow.
November 16, 2025 at 8:09 AM
I tried to install Openforld3 to my personal computer with pixi. It succeeded. I canceld the process because size of parameters were too big. So I will try again on HPC env tomorrow.
Reposted by pen(Taka)
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 got shuffled around different departments with no solution. It is really tough for me...
November 12, 2025 at 11:34 AM
I got shuffled around different departments with no solution. It is really tough for me...
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…
Era of open science
medium.com/@dapscience/...
medium.com/@dapscience/...
The Great Divergence: Why OpenFold3 Represents a New, Foundational Platform for Bio-AI
How the biopharma industry quietly reclaimed the future of scientific innovation.
medium.com
November 6, 2025 at 1:13 PM
Era of open science
medium.com/@dapscience/...
medium.com/@dapscience/...
Reposted by pen(Taka)
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...
Science is standing on the shoulders of giants.
I respect pior arts of all scientific researches.
I respect pior arts of all scientific researches.
November 6, 2025 at 12:48 PM
Science is standing on the shoulders of giants.
I respect pior arts of all scientific researches.
I respect pior arts of all scientific researches.
Photos from today’s running
November 3, 2025 at 12:38 PM
Photos from today’s running
I could have a fruitful discussion about AI driven drug discovery last week.
And found that main issue for promoting AI driven drug discovery is not changed over 20 years :P
It is a nightmare...
And found that main issue for promoting AI driven drug discovery is not changed over 20 years :P
It is a nightmare...
November 3, 2025 at 8:12 AM
I could have a fruitful discussion about AI driven drug discovery last week.
And found that main issue for promoting AI driven drug discovery is not changed over 20 years :P
It is a nightmare...
And found that main issue for promoting AI driven drug discovery is not changed over 20 years :P
It is a nightmare...
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…
Build environment from github repository with pixi #cheminformatics #memo #pixi
I could have really fruitful discussions last week at CBI2025 annual meeting. Really appreciate all participants and presenters. I realized that I love open science and I would like to contribute it 🙂 I wrote new…
I could have really fruitful discussions last week at CBI2025 annual meeting. Really appreciate all participants and presenters. I realized that I love open science and I would like to contribute it 🙂 I wrote new…
Build environment from github repository with pixi #cheminformatics #memo #pixi
I could have really fruitful discussions last week at CBI2025 annual meeting. Really appreciate all participants and presenters. I realized that I love open science and I would like to contribute it 🙂 I wrote new package for library management called pixi. In the previous post, I introduced pixi for making new environment. There are lots of github repositories are available and lots of codes are installed by pip, conda command.
iwatobipen.wordpress.com
November 1, 2025 at 10:31 AM
Build environment from github repository with pixi #cheminformatics #memo #pixi
I could have really fruitful discussions last week at CBI2025 annual meeting. Really appreciate all participants and presenters. I realized that I love open science and I would like to contribute it 🙂 I wrote new…
I could have really fruitful discussions last week at CBI2025 annual meeting. Really appreciate all participants and presenters. I realized that I love open science and I would like to contribute it 🙂 I wrote new…
CBI 2025 annual meeting is finished.
I hope every participants enjoyed tutorial of cheminformatics.
I hope every participants enjoyed tutorial of cheminformatics.
October 30, 2025 at 11:30 AM
CBI 2025 annual meeting is finished.
I hope every participants enjoyed tutorial of cheminformatics.
I hope every participants enjoyed tutorial of cheminformatics.
Check code availablity on several OS is really hard work. I respect all developers....
It's a really tough work for me.
It's a really tough work for me.
October 25, 2025 at 7:51 AM
Check code availablity on several OS is really hard work. I respect all developers....
It's a really tough work for me.
It's a really tough work for me.
Reposted by pen(Taka)
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...
Mt. Fuji is wearing a white hat
October 22, 2025 at 11:29 PM
Mt. Fuji is wearing a white hat
Reposted by pen(Taka)
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.
I enjoyed scientific coding training today!
October 22, 2025 at 12:12 PM
I enjoyed scientific coding training today!