Introducing The Structural History of Eukarya (SHE): The first proteome-scale phylogeny constructed entirely from 3D structure.
We computed 300 trillion alignments across 1,542 species to map the tree of life. 🧵👇 (1/5)
07.02.2026 08:50 — 👍 83 🔁 40 💬 2 📌 0
Compbio Asia
Please spread the word:
We invite applications to a two-week Computational Biology workshop in Singapore, June 14-27.
This NSF-funded workshop brings together 16-20 US grad students with international peers.
Apply by March 21: compbioasia.net
🧵 Details below:
05.02.2026 17:22 — 👍 1 🔁 9 💬 2 📌 0
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.
02.02.2026 07:52 — 👍 6 🔁 2 💬 0 📌 0
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...
30.01.2026 06:11 — 👍 297 🔁 147 💬 4 📌 3
AmpliPhy improves gene trees by adding homologs without affecting alignments
In phylogenomics, gene tree reconstruction depends on multiple sequence alignment (MSA) and tree inference, and ongoing work continues to improve inference quality. Denser taxon sampling has been associated with improved gene tree inference, suggesting that adding homologs could be a practical route to higher accuracy as sequence databases continue to expand. However, adding sequences can influence multiple steps of typical inference pipelines, and little is known on its specific effect on the multiple sequence alignment, tree reconstruction, and rooting steps. We performed a large-scale empirical benchmark to quantify how homolog enrichment affects alignment and phylogenetic inference. Using an enrichment-impoverishment design and a measure of tree accuracy based on taxonomic congruence, we found that enrichment consistently improves tree inference quality, while effects on alignment quality are marginal. We show that this improvement is associated with accurate root placement on enriched trees when sensitive homolog search is accompanied. Notably, much of the benefit can be retained with relatively compact alignments produced by sequence addition. Building on these observations, we provide a tool, AmpliPhy, which efficiently improves phylogenetic reconstruction of protein families through homolog enrichment. The AmpliPhy open-source pipeline software is available at https://github.com/DessimozLab/ampliphy. ### Competing Interest Statement The authors have declared no competing interest. Swiss National Science Foundation, https://ror.org/00yjd3n13, 216623, 10005715
Can ever-increasing sequence databases improve phylogenetic reconstruction of a gene family? Our new preprint introduces AmpliPhy, a pipeline that automates homolog enrichment to improve gene tree inference, built on a robust phylogenomic benchmark scheme. 🧵1/n
📃 doi.org/10.64898/2026.01.26.701724
28.01.2026 06:10 — 👍 25 🔁 14 💬 1 📌 0
Milot’s venture into establishing his own lab is incredibly excitinge. I highly recommend to join Milot on his mission to advance molecular biology through open-source bioinformatics.
21.01.2026 03:37 — 👍 36 🔁 3 💬 0 📌 0
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
20.01.2026 11:07 — 👍 105 🔁 54 💬 7 📌 1
In remembrance of Peer Bork | EMBL
EMBL and its community are deeply saddened by the death of Peer Bork, the organisation’s Interim Director General.
This is very sad news
'It is with great sadness that EMBL announces that Interim Director General Professor Peer Bork passed away from natural causes on 16 January 2026.'
www.embl.org/news/embl-an...
16.01.2026 18:06 — 👍 30 🔁 10 💬 3 📌 2
Phold's manuscript is now available @narjournal.bsky.social thanks to @susiegriggo.bsky.social @npbhavya.bsky.social @vijinim.bsky.social @linsalrob.bsky.social @martinsteinegger.bsky.social @milot.bsky.social @eunbelivable.bsky.social & others not on bsky #phagesky academic.oup.com/nar/article/...
14.01.2026 05:10 — 👍 82 🔁 44 💬 1 📌 1
Happy to share that our work on HLp, a bacterial histone from Leptospira perolatii, is now published in Nature Communications 🎉
In this study, we show that HLp forms stable tetramers that wrap ~60 bp of DNA, revealing a distinct histone–DNA organization in bacteria.
www.nature.com/articles/s41...
13.12.2025 08:09 — 👍 54 🔁 16 💬 2 📌 1
Today marks one year since the Dec. 3, 2024 martial law declaration that rocked South Korea and still reverberates today. What’s on my mind today is the grit of South Koreans who rushed to the National Assembly that night, in freezing weather, to demand a return to democratic government.
03.12.2025 03:09 — 👍 2169 🔁 549 💬 24 📌 21
We are deeply saddened to learn of the passing of Amos Bairoch. His vision and leadership helped build the foundations of today’s bioinformatics community. From the creation of essential biological databases to decades of mentorship, his influence can be felt across research groups worldwide.
02.12.2025 17:00 — 👍 4 🔁 2 💬 1 📌 1
LoL-align: sensitive and fast probabilistic protein structure alignment https://www.biorxiv.org/content/10.1101/2025.11.24.690091v1
26.11.2025 02:46 — 👍 12 🔁 7 💬 0 📌 0
AlphaFold Protein Structure Database 2025: a redesigned interface and updated structural coverage
Abstract. The AlphaFold Protein Structure Database (AFDB; https://alphafold.ebi.ac.uk), developed by EMBL–EBI and Google DeepMind, provides open access to
From Sameer Velankar & colleagues in @narjournal.bsky.social #NARDatabaseIssue | #AlphaFold #Protein #Structure #Database 2025: a redesigned interface and updated structural coverage | #Bioinformatics #Proteomics #OpenScience #AFDB 🧪🔓 CC/ @ebi.embl.org
⬇️
academic.oup.com/nar/advance-...
24.11.2025 00:56 — 👍 30 🔁 14 💬 0 📌 0
A few py2Dmol updates 🧬
py2dmol.solab.org
Integration with AlphaFoldDB (will auto fetch results). Drag and drop results from AF3-server or ColabFold for interactive experience! (1/4)
19.11.2025 08:15 — 👍 103 🔁 31 💬 1 📌 0
Congrats Spyro!
15.11.2025 07:10 — 👍 1 🔁 0 💬 1 📌 0
Guess the news is officially out! Extremely excited to announce that I will be starting my own laboratory at Institut Pasteur @pasteur.fr this coming spring!
Slight change to my office window view from Tokyo Tower🗼 to the Tour Eiffel. 🇫🇷
15.11.2025 06:42 — 👍 110 🔁 11 💬 28 📌 0
I want to spell this out in case the implications aren't clear:
This means all public tools/webapps of GISAID data (all the ones you've been used to seeing thru the pandemic, as far as we can tell) are prohibited.
The file allowed this. Cut that - cut off all tools the public & others were using.
07.11.2025 14:41 — 👍 258 🔁 136 💬 2 📌 8
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👇
28.10.2025 18:30 — 👍 125 🔁 42 💬 1 📌 3
GitHub - bbuchfink/diamond: Accelerated BLAST compatible local sequence aligner.
Accelerated BLAST compatible local sequence aligner. - bbuchfink/diamond
DIAMOND v2.1.15 now supports all taxonomy features for BLAST databases, and support for using BLAST databases has also been added to the Bioconda version github.com/bbuchfink/di...
28.10.2025 16:45 — 👍 16 🔁 5 💬 0 📌 0
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...
28.10.2025 05:58 — 👍 25 🔁 5 💬 1 📌 2
Working on the protein-hunter-chai google colab notebook. 😈
@yehlincho.bsky.social
28.10.2025 03:34 — 👍 33 🔁 5 💬 0 📌 0
Excited to release BoltzGen which brings SOTA folding performance to binder design! The best part of this project is collaborating with a broad network of leading wetlabs that test BoltzGen at an unprecedented scale, showing success on many novel targets and pushing the model to its limits!
26.10.2025 22:40 — 👍 103 🔁 41 💬 3 📌 5
We train machine learning models on millions of proteins. But when it comes to making predictions, do we need them to understand all proteins at once? Often, we need an accurate model for the specific protein we are studying or designing. We address this with ProteinTTT arxiv.org/abs/2411.02109 1/🧵
23.10.2025 13:08 — 👍 68 🔁 25 💬 2 📌 0
End-to-end protein design in the browser through evedesign. Generate and interactively explore designs in 2D/3D and export them as codon-optimized DNA. The underlying open source framework (released soon) is build to easily add new methods, more on that soon.
🌐 evedesign.bio
22.10.2025 14:30 — 👍 93 🔁 29 💬 2 📌 1
Announcing our new protein design server evedesign.bio:
• End-to-end protein design for everyone!
• Analyze your generated library interactively and on 3D structures
• Export codon-optimized DNA sequences for experimental testing.
22.10.2025 14:17 — 👍 7 🔁 2 💬 1 📌 0
We (@sobuelow.bsky.social) developed AF-CALVADOS to integrate AlphaFold and CALVADOS to simulate flexible multidomain proteins at scale
See preprint for:
— Ensembles of >12000 full-length human proteins
— Analysis of IDRs in >1500 TFs
📜 doi.org/10.1101/2025...
💾 github.com/KULL-Centre/...
20.10.2025 11:26 — 👍 92 🔁 37 💬 1 📌 1
Does it have any Foldseek hits? Just search against all databases in the webserver (with the profile/iterative search ideally).
17.10.2025 08:46 — 👍 0 🔁 0 💬 1 📌 0
One man's trash is another's treasure :)
17.10.2025 08:02 — 👍 0 🔁 0 💬 1 📌 0
Assistant Professor at GaTech CSE. Computational Biology and Machine Learning. UIUC PhD'21. Tsinghua BS'16
A natural product chemist using mass spec to discover chemical diversities in nature.
Working at Sookmyung Women's University, Seoul, Korea as an associate professor.
Virologist & Assistant Professor / Evolutionary Computational Structural Biology & Artificial Intelligence / One Health Virology 🦠@IBSquare/Vrije University Brussel (VUB) @vubrussel.bsky.social
Predoctoral Research Assistant at the Llorca lab @cniostopcancer.bsky.social working on mTORC1 signaling and cryo-EM ❄️🔬. Intrigued by the structural mechanisms of protein assemblies involved in endomembrane signaling and trafficking 🧪.
fungal taxonomist • PhD • Ukrainian expat • melancholic for all the good reasons • he/him
Biomed PhD | Co-Founder & CSO @ Drylab AI | Love insights on biotech trends & innovation | Iced coffee enthusiast 🧊☕
Assistant Professor @ucf.bsky.social
https://medvedev-lab.cs.ucf.edu/
Alumni @utswtxid.bsky.social
Computational Biology | Bionformatics | Cancer Biology
PostDoc in Computational Protein Design & Molecular Modeling at BIOC from École Polytechnique & IFPEN | PhD from Université de Franche-Comté
Postdoc with Sascha Martens and Tim Clausen at the Vienna BioCenter (VBC). #MSCA Fellow. Formerly University of Oxford and University of Antwerp.
Computational biologist and mechanistic interpretability researcher. For more find me at: https://mclarke1991.github.io & https://www.linkedin.com/in/matthew-alan-clarke/
PhD student @soreklab.bsky.social at Weizmann Institute of Science
Evolution of immune systems 🌱🦠
(he/him) Former PhD student / Postdoc @ Korbel group, EMBL.
Protein ML person, mathematics & science enthusiast.
developer of salad
preprint: https://www.biorxiv.org/content/10.1101/2025.01.31.635780v1
code: https://github.com/mjendrusch/salad
Research Fellow @flatironinstitute.org @simonsfoundation.org
Formerly @csail.mit.edu @msftresearch.bsky.social @uconn.bsky.social
Computational systems x structure biology | he/him | https://samsl.io | 👨🏼💻
single-molecule microbiology lab @ ITQB NOVA in Portugal
https://zach-hensel.github.io/
Computational biologist; Associate Prof. at University of Wisconsin-Madison; Jeanne M. Rowe Chair at Morgridge Institute
AI/ML researcher in biomedical sciences || enjoyer of image analysis, process automation, critical theory and food || opinions are my own to the best of my knowledge || they/them
Interested in protein structure and evolution. Somehow what they call a "PI" now, not sure how that happened. Hiring!
Plant Immunologist x Machine Learning, occasional biochemist | 🌱-🧫 interactions | UC Berkeley Postdoc | 2 x USDA NIFA Fellow
PhD student (MRC-UofG CVR)
🏰 antiviral defence | 🧬 evolution | 🔮 protein structure prediction
Researcher at CNRS interested in the biophysics of proteins. Modelling membrane proteins and their interaction with ligands. Working in Paris.
