Yoshitaka Moriwaki
@agsmith.bsky.social
とある文京区のJKラボォです。タンパク質の立体構造とバイオインフォマティクスに興味があります。I'm interested in protein bioinformatics. ORCID: 0000-0003-0448-9790
Reposted by Yoshitaka Moriwaki
My time in @martinsteinegger.bsky.social's group is ending, but I’m staying in Korea to build a lab at Sungkyunkwan University School of Medicine. If you or someone you know is interested in molecular machine learning and open-source bioinformatics, please reach out. I am hiring!
mirdita.org
mirdita.org
Mirdita Lab - Laboratory for Computational Biology & Molecular Machine Learning
Mirdita Lab builds scalable bioinformatics methods.
mirdita.org
January 20, 2026 at 11:07 AM
My time in @martinsteinegger.bsky.social's group is ending, but I’m staying in Korea to build a lab at Sungkyunkwan University School of Medicine. If you or someone you know is interested in molecular machine learning and open-source bioinformatics, please reach out. I am hiring!
mirdita.org
mirdita.org
Distance-Restraint-Guided Diffusion Models for Sampling Protein Conformational Changes and Ligand Dissociation Pathways
Tatsuki Hori, Yoshitaka Moriwaki, Ryuichiro Ishitani
www.biorxiv.org/content/10.6...
Our new preprint is out.
Tatsuki Hori, Yoshitaka Moriwaki, Ryuichiro Ishitani
www.biorxiv.org/content/10.6...
Our new preprint is out.
www.biorxiv.org
February 2, 2026 at 7:52 AM
Distance-Restraint-Guided Diffusion Models for Sampling Protein Conformational Changes and Ligand Dissociation Pathways
Tatsuki Hori, Yoshitaka Moriwaki, Ryuichiro Ishitani
www.biorxiv.org/content/10.6...
Our new preprint is out.
Tatsuki Hori, Yoshitaka Moriwaki, Ryuichiro Ishitani
www.biorxiv.org/content/10.6...
Our new preprint is out.
Reposted by Yoshitaka Moriwaki
FoldMason is out now in @science.org. It generates accurate multiple structure alignments for thousands of protein structures in seconds. Great work by Cameron L. M. Gilchrist and @milot.bsky.social.
📄 www.science.org/doi/10.1126/...
🌐 search.foldseek.com/foldmason
💾 github.com/steineggerla...
📄 www.science.org/doi/10.1126/...
🌐 search.foldseek.com/foldmason
💾 github.com/steineggerla...
Multiple protein structure alignment at scale with FoldMason
Protein structure is conserved beyond sequence, making multiple structural alignment (MSTA) essential for analyzing distantly related proteins. Computational prediction methods have vastly extended ou...
www.science.org
January 30, 2026 at 6:11 AM
FoldMason is out now in @science.org. It generates accurate multiple structure alignments for thousands of protein structures in seconds. Great work by Cameron L. M. Gilchrist and @milot.bsky.social.
📄 www.science.org/doi/10.1126/...
🌐 search.foldseek.com/foldmason
💾 github.com/steineggerla...
📄 www.science.org/doi/10.1126/...
🌐 search.foldseek.com/foldmason
💾 github.com/steineggerla...
I submitted this manuscript to a famous journal, but after 2 months, I received an e-mail saying that the editor who originally assigned to it became unavailable and sufficient reviewers have not been assigned yet. I have finally withdrawn this submission and am considering to another journal🤯
Our new preprint is out. Our group performed a comprehensive protein–protein complex prediction within 2,437 biosynthetic gene clusters. We predicted a total of 487,828 complexes for known BGCs, identifying 15,438 heteromeric interactions with an ipTM ≥ 0.6. (2/3)
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Predicting protein complexes in biosynthetic gene clusters
Biosynthetic gene clusters (BGCs) are contiguous genomic regions that encode diverse, non-homologous proteins required for the production of specific natural products. Their genetic diversity underlie...
www.biorxiv.org
January 27, 2026 at 3:58 AM
I submitted this manuscript to a famous journal, but after 2 months, I received an e-mail saying that the editor who originally assigned to it became unavailable and sufficient reviewers have not been assigned yet. I have finally withdrawn this submission and am considering to another journal🤯
mmCIF Rainbow Columns (VS Code Extension)
marketplace.visualstudio.com/items?itemNa...
It is designed to make reading and editing complex loop_ blocks easier. Unlike existing CIF editors or syntax highlighters, this extension focuses on human-readable visualization of mmCIF loop columns.
marketplace.visualstudio.com/items?itemNa...
It is designed to make reading and editing complex loop_ blocks easier. Unlike existing CIF editors or syntax highlighters, this extension focuses on human-readable visualization of mmCIF loop columns.
Rainbow mmCIF - Visual Studio Marketplace
Extension for Visual Studio Code - Column-based coloring for mmCIF loops.
marketplace.visualstudio.com
December 26, 2025 at 2:46 AM
mmCIF Rainbow Columns (VS Code Extension)
marketplace.visualstudio.com/items?itemNa...
It is designed to make reading and editing complex loop_ blocks easier. Unlike existing CIF editors or syntax highlighters, this extension focuses on human-readable visualization of mmCIF loop columns.
marketplace.visualstudio.com/items?itemNa...
It is designed to make reading and editing complex loop_ blocks easier. Unlike existing CIF editors or syntax highlighters, this extension focuses on human-readable visualization of mmCIF loop columns.
AmberTools 25 is now available on Homebrew🎉
brew install brewsci/bio/ambertools
brew install brewsci/bio/ambertools
December 20, 2025 at 4:33 PM
AmberTools 25 is now available on Homebrew🎉
brew install brewsci/bio/ambertools
brew install brewsci/bio/ambertools
The Terada and Leow groups have developed ColabReaction, a cloud-based tool that accelerates transition-state searches using the machine learning potential UMA. This work was featured as a journal cover.
available at: colabreaction.net
pubs.acs.org/doi/10.1021/...
available at: colabreaction.net
pubs.acs.org/doi/10.1021/...
November 11, 2025 at 11:00 AM
The Terada and Leow groups have developed ColabReaction, a cloud-based tool that accelerates transition-state searches using the machine learning potential UMA. This work was featured as a journal cover.
available at: colabreaction.net
pubs.acs.org/doi/10.1021/...
available at: colabreaction.net
pubs.acs.org/doi/10.1021/...
This paper has been published in ACS Omega: pubs.acs.org/doi/10.1021/...
Available at Google Colaboratory: github.com/cddlab/colab...
Available at Google Colaboratory: github.com/cddlab/colab...
November 10, 2025 at 5:56 AM
This paper has been published in ACS Omega: pubs.acs.org/doi/10.1021/...
Available at Google Colaboratory: github.com/cddlab/colab...
Available at Google Colaboratory: github.com/cddlab/colab...
Reposted by Yoshitaka Moriwaki
OpenFold3-preview (OF3p) is out: a sneak peek of our AF3-based structure prediction model. Our aim for OF3 is full AF3-parity for every modality. We now believe we have a clear path towards this goal and are releasing OF3p to enable building in the OF3 ecosystem. More👇
October 28, 2025 at 6:30 PM
OpenFold3-preview (OF3p) is out: a sneak peek of our AF3-based structure prediction model. Our aim for OF3 is full AF3-parity for every modality. We now believe we have a clear path towards this goal and are releasing OF3p to enable building in the OF3 ecosystem. More👇
Our new preprint is out. Our group performed a comprehensive protein–protein complex prediction within 2,437 biosynthetic gene clusters. We predicted a total of 487,828 complexes for known BGCs, identifying 15,438 heteromeric interactions with an ipTM ≥ 0.6. (2/3)
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Predicting protein complexes in biosynthetic gene clusters
Biosynthetic gene clusters (BGCs) are contiguous genomic regions that encode diverse, non-homologous proteins required for the production of specific natural products. Their genetic diversity underlie...
www.biorxiv.org
October 28, 2025 at 5:58 AM
Our new preprint is out. Our group performed a comprehensive protein–protein complex prediction within 2,437 biosynthetic gene clusters. We predicted a total of 487,828 complexes for known BGCs, identifying 15,438 heteromeric interactions with an ipTM ≥ 0.6. (2/3)
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Now DSSP 4.5.6 and its python module are available on Homebrew. `brew install brewsci/bio/dssp`.
> Since version 4.5.2 it is possible to build a Python module to directly work with DSSP info inside your Python scripts.
github.com/PDB-REDO/dssp
It can be installed using `brew install brewsci/bio/dssp`. I hope it will also be available on PyPI.
github.com/PDB-REDO/dssp
It can be installed using `brew install brewsci/bio/dssp`. I hope it will also be available on PyPI.
GitHub - PDB-REDO/dssp: Application to assign secondary structure to proteins
Application to assign secondary structure to proteins - PDB-REDO/dssp
github.com
October 28, 2025 at 5:48 AM
Now DSSP 4.5.6 and its python module are available on Homebrew. `brew install brewsci/bio/dssp`.
Dutch courage? Effects of acute alcohol consumption on self-ratings and observer ratings of foreign language skills
journals.sagepub.com/doi/10.1177/...
journals.sagepub.com/doi/10.1177/...
Sage Journals: Discover world-class research
Subscription and open access journals from Sage, the world's leading independent academic publisher.
journals.sagepub.com
September 19, 2025 at 5:53 AM
Dutch courage? Effects of acute alcohol consumption on self-ratings and observer ratings of foreign language skills
journals.sagepub.com/doi/10.1177/...
journals.sagepub.com/doi/10.1177/...
Reposted by Yoshitaka Moriwaki
「科学者はもはやTwitterが仕事の役に立たないと感じ、Blueskyに切り替えた」という新しい研究結果。
過去10年、Twitterは科学者の拠点だったが、マスクの買収によって疑似科学、陰謀論、嫌がらせが蔓延し、多くの科学者がTwitter(X)を見限って、Blueskyに移動。
この現象について改めて研究が行われ、実際「科学者はかつてTwitterから得ていた専門的な利益を、今はBlueskyでより効果的に得ている」というデータが示されている。
科学が弾圧される今、科学者フレンドリーなSNSとしてブルスカの成長に期待
academic.oup.com/icb/advance-...
過去10年、Twitterは科学者の拠点だったが、マスクの買収によって疑似科学、陰謀論、嫌がらせが蔓延し、多くの科学者がTwitter(X)を見限って、Blueskyに移動。
この現象について改めて研究が行われ、実際「科学者はかつてTwitterから得ていた専門的な利益を、今はBlueskyでより効果的に得ている」というデータが示されている。
科学が弾圧される今、科学者フレンドリーなSNSとしてブルスカの成長に期待
academic.oup.com/icb/advance-...
Scientists no Longer Find Twitter Professionally Useful, and have Switched to Bluesky
Synopsis. Social media has become widely used by the scientific community for a variety of professional uses, including networking and public outreach. For
academic.oup.com
August 21, 2025 at 1:32 AM
「科学者はもはやTwitterが仕事の役に立たないと感じ、Blueskyに切り替えた」という新しい研究結果。
過去10年、Twitterは科学者の拠点だったが、マスクの買収によって疑似科学、陰謀論、嫌がらせが蔓延し、多くの科学者がTwitter(X)を見限って、Blueskyに移動。
この現象について改めて研究が行われ、実際「科学者はかつてTwitterから得ていた専門的な利益を、今はBlueskyでより効果的に得ている」というデータが示されている。
科学が弾圧される今、科学者フレンドリーなSNSとしてブルスカの成長に期待
academic.oup.com/icb/advance-...
過去10年、Twitterは科学者の拠点だったが、マスクの買収によって疑似科学、陰謀論、嫌がらせが蔓延し、多くの科学者がTwitter(X)を見限って、Blueskyに移動。
この現象について改めて研究が行われ、実際「科学者はかつてTwitterから得ていた専門的な利益を、今はBlueskyでより効果的に得ている」というデータが示されている。
科学が弾圧される今、科学者フレンドリーなSNSとしてブルスカの成長に期待
academic.oup.com/icb/advance-...
Boltz-1の開発グループはDiffdockと同じグループなんだけど、なんでかDiffdockと性能比較していないね あとよく言われるAutodockとも。
するまでもなく性能良くなっているんだろうけれど、論文の査読者的には「なぜ比較していない？」って言うのかな
するまでもなく性能良くなっているんだろうけれど、論文の査読者的には「なぜ比較していない？」って言うのかな
August 19, 2025 at 6:28 AM
Boltz-1の開発グループはDiffdockと同じグループなんだけど、なんでかDiffdockと性能比較していないね あとよく言われるAutodockとも。
するまでもなく性能良くなっているんだろうけれど、論文の査読者的には「なぜ比較していない？」って言うのかな
するまでもなく性能良くなっているんだろうけれど、論文の査読者的には「なぜ比較していない？」って言うのかな
Reposted by Yoshitaka Moriwaki
Unexpectedly, @jurgjn.bsky.social found that running Alphafold3 predictions for protein interactions can yield ipTM scores that are more predictive of true interactions when run in pools of proteins instead of pairwise predictions. Presumably, this reflects some sort of "competition effect".
July 22, 2025 at 2:13 PM
Unexpectedly, @jurgjn.bsky.social found that running Alphafold3 predictions for protein interactions can yield ipTM scores that are more predictive of true interactions when run in pools of proteins instead of pairwise predictions. Presumably, this reflects some sort of "competition effect".
Reposted by Yoshitaka Moriwaki
DeepMind will fund CASP for a year. Very nice to hear.
(not paying Stat $30 a month, but you can read the first bit).
www.statnews.com/2025/07/21/c...
(not paying Stat $30 a month, but you can read the first bit).
www.statnews.com/2025/07/21/c...
AlphaFold developer Google DeepMind to fund CASP as NIH funding falls short
Protein structure prediction contest CASP gets temporary funding from Google DeepMind as NIH grant runs out.
www.statnews.com
July 22, 2025 at 5:13 AM
DeepMind will fund CASP for a year. Very nice to hear.
(not paying Stat $30 a month, but you can read the first bit).
www.statnews.com/2025/07/21/c...
(not paying Stat $30 a month, but you can read the first bit).
www.statnews.com/2025/07/21/c...
The Terada group, in collaboration with Dr. Leow, has developed ColabReaction — a cloud-based tool for accelerated transition state searches using Direct MaxFlux (DMF) and the ML potential (UMA)
available at: colabreaction.net
Preprint: chemrxiv.org/engage/chemr...
available at: colabreaction.net
Preprint: chemrxiv.org/engage/chemr...
Under construction
colabreaction.net
July 16, 2025 at 2:55 PM
The Terada group, in collaboration with Dr. Leow, has developed ColabReaction — a cloud-based tool for accelerated transition state searches using Direct MaxFlux (DMF) and the ML potential (UMA)
available at: colabreaction.net
Preprint: chemrxiv.org/engage/chemr...
available at: colabreaction.net
Preprint: chemrxiv.org/engage/chemr...
> Since version 4.5.2 it is possible to build a Python module to directly work with DSSP info inside your Python scripts.
github.com/PDB-REDO/dssp
It can be installed using `brew install brewsci/bio/dssp`. I hope it will also be available on PyPI.
github.com/PDB-REDO/dssp
It can be installed using `brew install brewsci/bio/dssp`. I hope it will also be available on PyPI.
GitHub - PDB-REDO/dssp: Application to assign secondary structure to proteins
Application to assign secondary structure to proteins - PDB-REDO/dssp
github.com
July 15, 2025 at 1:48 PM
> Since version 4.5.2 it is possible to build a Python module to directly work with DSSP info inside your Python scripts.
github.com/PDB-REDO/dssp
It can be installed using `brew install brewsci/bio/dssp`. I hope it will also be available on PyPI.
github.com/PDB-REDO/dssp
It can be installed using `brew install brewsci/bio/dssp`. I hope it will also be available on PyPI.
うーん、足の指を骨折してしまったかもしれん。ただの捻挫かと思ってたけど、すごく紫色に腫れてて痛い
外回りが増えてるから安静にできないのは困るな
外回りが増えてるから安静にできないのは困るな
May 24, 2025 at 2:22 PM
うーん、足の指を骨折してしまったかもしれん。ただの捻挫かと思ってたけど、すごく紫色に腫れてて痛い
外回りが増えてるから安静にできないのは困るな
外回りが増えてるから安静にできないのは困るな
Reposted by Yoshitaka Moriwaki
The CoVFit paper is now published @natcomms.nature.com !! Exciting work led by Jumpei Ito really showing the potential of pLMs for genotype-2-phenotype predictions!!
www.nature.com/articles/s41...
www.nature.com/articles/s41...
A protein language model for exploring viral fitness landscapes - Nature Communications
Ito et al. present CoVFit, an AI model that predicts variant fitness (transmissibility) from spike protein sequences alone. They further demonstrate its utility in forecasting viral evolution via sing...
www.nature.com
May 16, 2025 at 4:01 PM
The CoVFit paper is now published @natcomms.nature.com !! Exciting work led by Jumpei Ito really showing the potential of pLMs for genotype-2-phenotype predictions!!
www.nature.com/articles/s41...
www.nature.com/articles/s41...
大学に長年いると、数は少ないながらも実家暮らしの学生の中には、学部の選択、研究室、就職先の企業・業種に至るまで、親の意向に抗えず言いなりの人生を歩んでる子の話をそこそこ聞くことがある
大学入試かつ医学部ならまだ聞く話だが、それ以外でもあるのか、みたいな
大学入試かつ医学部ならまだ聞く話だが、それ以外でもあるのか、みたいな
May 13, 2025 at 3:02 AM
大学に長年いると、数は少ないながらも実家暮らしの学生の中には、学部の選択、研究室、就職先の企業・業種に至るまで、親の意向に抗えず言いなりの人生を歩んでる子の話をそこそこ聞くことがある
大学入試かつ医学部ならまだ聞く話だが、それ以外でもあるのか、みたいな
大学入試かつ医学部ならまだ聞く話だが、それ以外でもあるのか、みたいな
Our latest work has been published! Our additional implementation for Boltz-1 largely improves the stereochemical accuracy of predicted ligand molecule without retraining the model.
We also developed a notebook on Google Colaboratory, colab.research.google.com/github/cddla... .
We also developed a notebook on Google Colaboratory, colab.research.google.com/github/cddla... .
March 29, 2025 at 11:26 AM
Our latest work has been published! Our additional implementation for Boltz-1 largely improves the stereochemical accuracy of predicted ligand molecule without retraining the model.
We also developed a notebook on Google Colaboratory, colab.research.google.com/github/cddla... .
We also developed a notebook on Google Colaboratory, colab.research.google.com/github/cddla... .
なんか、引き受けるかどうか熟考を要するような無報酬の仕事依頼メールが1日に何個かくるようになって、本業が進みにくくなっているのを感じる
February 20, 2025 at 7:35 AM
なんか、引き受けるかどうか熟考を要するような無報酬の仕事依頼メールが1日に何個かくるようになって、本業が進みにくくなっているのを感じる
最近の選挙で、投票所の記名台近くで一人で投票券3枚持った写真が存在するのおかしくね？みたいな騒動あったけど、投票券を偽造して複数枚持ち込むって、そんなに難しいことではないように思えるから（本人確認もないし）、すでに組織的にやられてるんでは？と思った
November 21, 2024 at 12:51 AM
最近の選挙で、投票所の記名台近くで一人で投票券3枚持った写真が存在するのおかしくね？みたいな騒動あったけど、投票券を偽造して複数枚持ち込むって、そんなに難しいことではないように思えるから（本人確認もないし）、すでに組織的にやられてるんでは？と思った