pen(Taka)
@iwatobipen.bsky.social
📤 1145
📥 798
📝 416
Medicinal Chemist, Cheminformatician, Runner and ?
1 day ago
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Realy cooooooooooooooooool
add a skeleton here at some point
5 days ago
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My eldest son was able to finish the last tournament of the year with a victory. :)
5 days ago
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reposted by
pen(Taka)
Greg Landrum
6 days ago
Today's
#RDKit
blog post is a tutorial/explanation about which atoms are considered as candidates for tetrahedral chirality.
greglandrum.github.io/rdkit-blog/p...
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About tetrahedral chirality in the RDKit – RDKit blog
Answering a frequently asked question
https://greglandrum.github.io/rdkit-blog/posts/2025-12-21-Chiral-atoms.html
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5km run at morning
10 days ago
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reposted by
pen(Taka)
Greg Landrum
13 days ago
This week's
#RDKit
blog post, like last week's, looks at creating your own synthon spaces. Last week was BRICS, this week we use some combichem reactions:
greglandrum.github.io/rdkit-blog/p...
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Building synthon spaces with combinatorial reactions – RDKit blog
A frequently requested tutorial part 2
https://greglandrum.github.io/rdkit-blog/posts/2025-12-14-Reaction-synthons.html
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ourworldindata.org/grapher/cost...
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Cost of sequencing a full human genome
Cost of sequencing the full genetic information of a human, measured in US$. This data is not adjusted for inflation.
https://ourworldindata.org/grapher/cost-of-sequencing-a-full-human-genome
12 days ago
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Use joblib with free-threaded python
#memo
#diary
Python 3.14 was released on 7 October 2025. The new version of python support for free-threaded (No GIL). I asked it about AI and reasonable description shown below. To understand the merit of "No-GIL" Python (officially known as free-threaded…
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Use joblib with free-threaded python #memo #diary
Python 3.14 was released on 7 October 2025. The new version of python support for free-threaded (No GIL). I asked it about AI and reasonable description shown below. To understand the merit of "No-GIL" Python (officially known as free-threaded Python), we first need to quickly establish what the Global Interpreter Lock (GIL) is and why it has historically been a bottleneck.
https://iwatobipen.wordpress.com/2025/12/13/use-joblib-with-free-threaded-python-memo-diary/
14 days ago
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Suitable investments are required not only AI technology but also data collection technology to promote AI driven drug discovery (IMHO). Because data is new oil.
19 days ago
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reposted by
pen(Taka)
Chemjobber
23 days ago
There is quite a bit of AI skepticism on chemsky, and reasonably so - but it is very interesting to see /another/ chemistry AI startup (Excelsior Sciences) get bigtime funding ($95M):
cen.acs.org/physical-che...
by
@cenmag.bsky.social
's Aayushi Pratap
#chemchat
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New York AI chemistry start-up raises $95 million
Excelsior Sciences cofounders say the company will make new molecules using robots and artificial intelligence
https://cen.acs.org/physical-chemistry/computational-chemistry/New-York-AI-chemistry-start-up/103/web/2025/12
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The Latest in Automated Analog Generation | Science | AAAS
www.science.org/content/blog...
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The Latest in Automated Analog Generation
https://www.science.org/content/blog-post/latest-automated-analog-generation
20 days ago
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I started my blog post 16 years ago! It's really amazing that I can keep it :)
21 days ago
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ourworldindata.org/brief-histor...
Worth to read!
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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.
https://ourworldindata.org/brief-history-of-ai
about 1 month ago
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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…
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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 🙂
https://iwatobipen.wordpress.com/2025/11/23/similarity-screening-with-rdkit-rdkit-similarityscreener-memo-cheminformatics/
about 1 month ago
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12km jog ✅
about 1 month ago
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reposted by
pen(Taka)
Greg Landrum
about 1 month ago
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...
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Working with the LOBSTER Data set II – RDKit blog
Conformer generation and comparing 3D fingerprints
https://greglandrum.github.io/rdkit-blog/posts/2025-11-16-working-with-lobster-2.html
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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.
about 1 month ago
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www.fiercebiotech.com/biotech/pfiz...
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Pfizer's parade of pipeline cuts: Seagen, BioNTech and MASH programs among 11 axed
Pfizer has axed 11 programs including two pipeline assets from its $43 billion Seagen acquisition, work on a BioNTech-partnered mR | Pfizer has axed 11 programs including two pipeline assets from its ...
https://www.fiercebiotech.com/biotech/pfizers-parade-pipeline-cuts-seagen-biontech-and-mash-programs-among-11-axed
about 1 month ago
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reposted by
pen(Taka)
Greg Landrum
about 2 months ago
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...
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Working with the LOBSTER Data set I – RDKit blog
Registering and working with a 3D data set using lwreg
https://greglandrum.github.io/rdkit-blog/posts/2025-11-08-working-with-lobster-1.html
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www.fiercebiotech.com/biotech/lill...
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Lilly continues AI push, inking $100M-plus research pact with Insilico
Eli Lilly is inking a $100 million-plus biobucks deal with Insilico Medicine in hopes of using artificial intelligence to discover new drugs. | Eli Lilly is inking a $100 million-plus biobucks deal wi...
https://www.fiercebiotech.com/biotech/lilly-continues-ai-push-inking-100m-plus-research-pact-insilico
about 1 month ago
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www.fiercebiotech.com/biotech/take...
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Takeda pays Innovent $1.2B upfront, offers whopping $10B-plus in biobucks for cancer assets
Takeda is
https://www.fiercebiotech.com/biotech/takeda-pays-innovent-12b-upfront-rights-2-cancer-candidates?utm_source=email&utm_medium=email&utm_campaign=LS-NL-FierceOncology&oly_enc_id=0294C1237756H1E
about 1 month ago
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I got shuffled around different departments with no solution. It is really tough for me...
about 1 month ago
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share.google/gqyfuYGbYCbu...
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Preprint site arXiv is banning computer-science reviews: here’s why
The repository is taking steps to tackle a surge in low quality, AI-generated content.
https://share.google/gqyfuYGbYCbu7Ji6X
about 2 months ago
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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…
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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.
https://iwatobipen.wordpress.com/2025/11/09/install-roshambo2-to-pixi-env-memo-cheminformatics-rdkit/
about 2 months ago
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Era of open science
medium.com/@dapscience/...
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The Great Divergence: Why OpenFold3 Represents a New, Foundational Platform for Bio-AI
How the biopharma industry quietly reclaimed the future of scientific innovation.
https://medium.com/@dapscience/the-great-divergence-why-openfold3-represents-a-new-foundational-platform-for-bio-ai-72fd13b9a774
about 2 months ago
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reposted by
pen(Taka)
Greg Landrum
about 2 months ago
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...
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RDKit
Zulip organization for the RDKit community
https://rdkit.zulipchat.com/join/ay4ccupypzry2e2fr3m54guv/
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Science is standing on the shoulders of giants. I respect pior arts of all scientific researches.
about 2 months ago
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Photos from today’s running
about 2 months ago
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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...
about 2 months ago
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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…
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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.
https://iwatobipen.wordpress.com/2025/11/02/run-md-simulation-with-openffopenmm-on-pixis-env-cheminformatics-rdkit-pixi-memo/
about 2 months ago
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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…
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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.
https://iwatobipen.wordpress.com/2025/11/01/build-environment-from-github-repository-with-pixi-cheminformatics-memo-pixi/
about 2 months ago
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CBI 2025 annual meeting is finished. I hope every participants enjoyed tutorial of cheminformatics.
about 2 months ago
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Check code availablity on several OS is really hard work. I respect all developers.... It's a really tough work for me.
2 months ago
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reposted by
pen(Taka)
Greg Landrum
2 months ago
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...
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Using the RDKit in a C++ program – RDKit blog
It’s actually pretty easy
https://greglandrum.github.io/rdkit-blog/posts/2021-07-24-setting-up-a-cxx-dev-env.html
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Mt. Fuji is wearing a white hat
2 months ago
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reposted by
pen(Taka)
Greg Landrum
2 months ago
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.
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I enjoyed scientific coding training today!
2 months ago
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Try to use new package manager for python
#pixi
#memo
October has arrived, and Japan has become quite cool. It's a great season for running now. By the way, package management is important task for lots of data scientists. Becase they use lots of packages and each packages depend on other…
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Try to use new package manager for python #pixi #memo
October has arrived, and Japan has become quite cool. It's a great season for running now. By the way, package management is important task for lots of data scientists. Becase they use lots of packages and each packages depend on other packages. Especially CUDA, I often struggle the issues. Anaconda is one of the useful package manager but it takes long time for solving dependency sometime.
https://iwatobipen.wordpress.com/2025/10/12/try-to-use-new-package-manager-for-python-pixi-memo/
3 months ago
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Photo from today’s my running course.
3 months ago
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reposted by
pen(Taka)
Ewan Birney
3 months ago
I am hiring! - looking for a Staff Scientist to co-run my research group with me. Staff Scientist is a senior professional scientist role at EMBL. Please forward to people you might know who could be interested!
embl.wd103.myworkdayjobs.com/en-US/EMBL/j...
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Staff Scientist
About EMBL-EBI EMBL’s European Bioinformatics Institute is a data powerhouse, utilised on a global scale to advance scientific discovery through bioinformatics and solutions to some of the world’s mos...
https://embl.wd103.myworkdayjobs.com/en-US/EMBL/job/Staff-Scientist_JR2425
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It seems interesting approach for generating seaquence with backbone of protein and non protein elements information. Is it will be new approach for induced docking?
openreview.net/forum?id=8tQ...
3 months ago
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forbesjapan.com/articles/det...
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AIの時代に求められる賢明なリーダーシップとは | Forbes JAPAN 公式サイト(フォーブス ジャパン)
スコット・オールドリッジ氏はIP Servicesの最高経営責任者(CEO)であり、ビジョナリーリーダーでベストセラー「VisibleOps Cybersecurity」の著者である。「道具を持った愚か者は、依然として愚か者である」という古...
https://forbesjapan.com/articles/detail/82548
3 months ago
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reposted by
pen(Taka)
Tony L.
5 months ago
I wrote about it in a blog post here:
tlint101.github.io/practice-in-...
(It is basically the tutorial section, but it counts!)
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Practice in Code - Announcing the pharmacophore-toolkit!
https://tlint101.github.io/practice-in-code/posts/13-Announcing-pharmacophore-toolkit.html
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reposted by
pen(Taka)
Tony L.
5 months ago
My first post and I would like to plug my project - pharmacophore-toolkit. I thought others in the
#cheminformatics
,
#molecularmodeling
,
#drugdiscovery
, or the
#chemsky
#compchem
community would find it helpful.
github.com/tlint101/pha...
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GitHub - tlint101/pharmacophore-toolkit: Generate simple pharmacophore models from RDKit
Generate simple pharmacophore models from RDKit. Contribute to tlint101/pharmacophore-toolkit development by creating an account on GitHub.
https://github.com/tlint101/pharmacophore-toolkit
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AI is an extremely useful tool, but it consumes vast amounts of energy and impacts the environment. Can we balance technological progress with environmental conservation?
3 months ago
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Neurons can communicate via hidden network of nanotubes, study finds | Science | AAAS
www.science.org/content/arti...
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Neurons can communicate via hidden network of nanotubes, study finds
Tubes in mouse and human brains may also influence spread of brain disease
https://www.science.org/content/article/neurons-can-communicate-hidden-network-nanotubes-study-finds?utm_source=sfmc&utm_medium=email&utm_campaign=ScienceAdviser&utm_content=distillation&et_rid=677275354&et_cid=5750009
3 months ago
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Now we can use compiled version of mmseq from original repo.
github.com/soedinglab/m...
I would like to test the perfomance on HPC environment.
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GitHub - soedinglab/MMseqs2: MMseqs2: ultra fast and sensitive search and clustering suite
MMseqs2: ultra fast and sensitive search and clustering suite - soedinglab/MMseqs2
https://github.com/soedinglab/mmseqs2
3 months ago
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www.unesco.org/en/artificia...
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Ethics of Artificial Intelligence
The Recommendation
https://www.unesco.org/en/artificial-intelligence/recommendation-ethics?hub=32618
3 months ago
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Leveraging Structural and Computational Biology for Molecular Glue Discovery | Journal of Medicinal Chemistry
pubs.acs.org/doi/10.1021/...
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Leveraging Structural and Computational Biology for Molecular Glue Discovery
The discovery of molecular glues has made significant strides, unlocking new avenues for targeted protein degradation as a therapeutic strategy, thereby expanding the scope of drug discovery into terr...
https://pubs.acs.org/doi/10.1021/acs.jmedchem.5c00076
3 months ago
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reposted by
pen(Taka)
Greg Landrum
3 months ago
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...
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Drawing simple protein–ligand interaction diagrams with the RDKit – RDKit blog
Quick, but useful
https://greglandrum.github.io/rdkit-blog/posts/2025-09-26-drawing-interactions-1.html
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