Yoshitaka Moriwaki

Mirdita Lab - Laboratory for Computational Biology & Molecular Machine Learning Mirdita Lab builds scalable bioinformatics methods.

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

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.

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...

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...

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 I have finally withdrawn this submission and am considering to another journal🤯

Rainbow mmCIF - Visual Studio Marketplace Extension for Visual Studio Code - Column-based coloring for mmCIF loops.

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.

AmberTools 25 is now available on Homebrew🎉
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/...

This paper has been published in ACS Omega: pubs.acs.org/doi/10.1021/...
Available at Google Colaboratory: github.com/cddlab/colab...

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👇

GitHub - DunbrackLab/IPSAE: Scoring function for interprotein interactions in AlphaFold2 and AlphaFold3 Scoring function for interprotein interactions in AlphaFold2 and AlphaFold3 - DunbrackLab/IPSAE

We used the ipSAE metric developed by @rolanddunbrack.bsky.social ( github.com/DunbrackLab/... ) alongside ipTM to evaluate the predicted complexes. We found that ipSAE showed greater discriminative power than ipTM in identifying true binding pairs among highly similar proteins. (3/3)

Among them, 1,390 protein pairs exhibited structural homology with an RMSD ≤ 2.0 Å. These predictions highlight intriguing molecular mechanisms involving proteins previously annotated as uncharacterized or potentially dysfunctional. (2/3)

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...

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...

Now DSSP 4.5.6 and its python module are available on Homebrew. `brew install brewsci/bio/dssp`.

> Participants who consumed alcohol had significantly better observer-ratings for their Dutch language, specifically better pronunciation, compared with those who did not consume alcohol. However, alcohol had no effect on self-ratings of Dutch language skills.

Sage Journals: Discover world-class research Subscription and open access journals from Sage, the world's leading independent academic publisher.

Dutch courage? Effects of acute alcohol consumption on self-ratings and observer ratings of foreign language skills
journals.sagepub.com/doi/10.1177/...

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

「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-...

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

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".

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.

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...

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...

GitHub - PDB-REDO/dssp: Application to assign secondary structure to proteins Application to assign secondary structure to proteins - PDB-REDO/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.

ええ？そちらもですか？？やーばいでしょ
てかA.R.E.を当てにして見切り発車している施策がどの大学でも多くないですかね

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

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...

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...

私は育ちが広島だったので、関東の恐ろしい受験戦争の話を聞くと本当にビビるんですが、関東育ちは「いやそれくらい当たり前でしょ」「終わったら笑い話になるよ」みたいな感じになってて二重にビビりますわ　勉強させることの意味はまだわかるんですが、「勉強しないと死ぬよ」みたいなのは洗脳ですわ

こっとさんもそういう経緯があったのですね。九州は……まぁそういう土地柄というのもある。。
でもいずれにしても、どこかで親から反抗して独立しないといけないと思います。下手すると博士課程D3になっても親元に現在と将来を監視されている子もいないわけではないですからね

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

やりますねぇ！！！おめでとうございます！

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... .