A few py2Dmol updates π§¬
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 β π 100 π 29 π¬ 1 π 0
Congrats Spyro!
15.11.2025 07:10 β π 1 π 0 π¬ 1 π 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 TowerπΌ to the Tour Eiffel. π«π·
15.11.2025 06:42 β π 105 π 11 π¬ 27 π 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 β π 256 π 142 π¬ 2 π 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. Moreπ
28.10.2025 18:30 β π 126 π 42 π¬ 1 π 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 β π 16 π 5 π¬ 0 π 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 proteinβprotein 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 β₯ 0.6. (2/3)
www.biorxiv.org/content/10.1...
28.10.2025 05:58 β π 24 π 5 π¬ 1 π 1
Working on the protein-hunter-chai google colab notebook. π
@yehlincho.bsky.social
28.10.2025 03:34 β π 33 π 5 π¬ 0 π 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 β π 103 π 41 π¬ 3 π 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/π§΅
23.10.2025 13:08 β π 68 π 25 π¬ 2 π 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.
π evedesign.bio
22.10.2025 14:30 β π 92 π 30 π¬ 2 π 1
Announcing our new protein design server evedesign.bio:
β’ End-to-end protein design for everyone!
β’ Analyze your generated library interactively and on 3D structures
β’ Export codon-optimized DNA sequences for experimental testing.
22.10.2025 14:17 β π 7 π 2 π¬ 1 π 0
We (@sobuelow.bsky.social) developed AF-CALVADOS to integrate AlphaFold and CALVADOS to simulate flexible multidomain proteins at scale
See preprint for:
β Ensembles of >12000 full-length human proteins
β Analysis of IDRs in >1500 TFs
π doi.org/10.1101/2025...
πΎ github.com/KULL-Centre/...
20.10.2025 11:26 β π 89 π 37 π¬ 0 π 0
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 β π 0 π 0 π¬ 1 π 0
One man's trash is another's treasure :)
17.10.2025 08:02 β π 0 π 0 π¬ 1 π 0
Our Metabuli taxonomic classifier is now available as an app compatible with Windows, Linux, and macOS. It features an interactive visualization developed by @sunjaelee.bsky.social, along with improvements to Metabuli by @jbeom.bsky.social.
π academic.oup.com/bioinformati...
16.10.2025 13:01 β π 25 π 8 π¬ 0 π 0
Easy and interactive taxonomic profiling with Metabuli App.
It integrates database curation, read QC, taxonomic profiling, and visualization right on your desktop.
No command line, server, or internet required.
Now published in Bioinformatics! π§΅1/5
doi.org/10.1093/bioi...
github.com/steineggerla...
16.10.2025 07:29 β π 24 π 11 π¬ 1 π 1
Easy and interactive taxonomic profiling with Metabuli App academic.oup.com/bioinformati... π§¬π₯οΈπ§ͺ github.com/steineggerla...
14.10.2025 17:55 β π 15 π 5 π¬ 0 π 0
AFDB v6 is already available in Foldseek!
π search.foldseek.com
foldseek databases Alphafold/UniProt50 afdb50 tmp
foldseek easy-search query.cif afdb50 res.m8 tmp --cluster-search 0/1 (Reps only / all 241M)
Thanks @ebi.embl.org and DeepMind for working with us to make it available to everyone.
07.10.2025 14:33 β π 23 π 2 π¬ 0 π 0
Weβre renewing our collaboration with Google DeepMind!
We'll keep developing the AlphaFold Database to support protein science worldwide π
To mark the moment weβve synchronised the database with UniProtKB release 2025_03.
www.ebi.ac.uk/about/news/t...
π₯οΈπ§¬ #AlphaFold
@pdbeurope.bsky.social
07.10.2025 14:03 β π 74 π 17 π¬ 0 π 2
#RECOMB2026 will be in Thessaloniki, Greece on May 26-29, 2026. Satellites on May 24-25. Save the date!
΀ο ΟΟ
Ξ½ΞΞ΄ΟΞΉΞΏ #RECOMB2026 ΞΈΞ± ΟΟΞ±Ξ³ΞΌΞ±ΟΞΏΟοιηθΡί ΟΟΞ· ΞΞ΅ΟΟαλονίκη, ΟΟΞΉΟ 26-29 ΞΞ±ΞΞΏΟ
2026. ΞΞΉ δοΟΟ
ΟΞΏΟΞΉΞΊΞΟ Ξ΅ΞΊΞ΄Ξ·Ξ»ΟΟΞ΅ΞΉΟ ΞΈΞ± διΡξαΟΞΈΞΏΟΞ½ ΟΟΞΉΟ 24-25 ΞΞ±ΞΞΏΟ
2026. ΣημΡιΟΟΟΞ΅ ΟΞ·Ξ½ Ξ·ΞΌΞ΅ΟΞΏΞΌΞ·Ξ½Ξ―Ξ±!
26.09.2025 15:03 β π 23 π 13 π¬ 0 π 1
HHMI adopts Plan U journals.plos.org/plosbiology/...
24.09.2025 18:08 β π 151 π 70 π¬ 9 π 16
GPU-accelerated homology search with MMseqs2 - Nature Methods
Graphics processing unit-accelerated MMseqs2 offers tremendous speedups for homology retrieval from metagenomic databases, query-centered multiple sequence alignment generation for structure predictio...
MMseqs2-GPU sets new standards in single query search speed, allows near instant search of big databases, scales to multiple GPUs and is fast beyond VRAM. It enables ColabFold MSA generation in seconds and sub-second Foldseek search against AFDB50. 1/n
π www.nature.com/articles/s41...
πΏ mmseqs.com
21.09.2025 08:06 β π 174 π 64 π¬ 4 π 2
Happy to see that Spacedust is now published on Nature Methods!
It combines sensitive Foldseek structure search and conserved neighborhood detection to discover functionally-associated gene clusters in prokaryotic & viral genomes.
1/6π§΅
16.09.2025 20:26 β π 21 π 12 π¬ 1 π 0
Preprint:
Highly efficient protein structure prediction on NVIDIA RTX Blackwell and Grace-Hopper
nvda.ws/4n4xzz9
Visit the NVIDIA Digital Biology Labs website to find more information like this:
t.co/R9ufEZrGEA
16.09.2025 13:59 β π 14 π 4 π¬ 0 π 0
Here for #bioinformatics / #computationalBiology of #Genomics, #Oncology and #Virology. Also loves #dataViz and open-source software.
Virologist, Chief Editor of Frontiers in Virology.
Emeritus & Visiting Professor of Tokushima University, Japan.
Foodie. Cat lover. Big fan of Japanese temples, shrines and castles.
https://www.frontiersin.org/journals/virology
PhD student in the Schatz lab @ Johns Hopkins University
From Pipette to Python | Drug & Protein Design | Structural Biology
Bioinformatics Group leader at Institute of Integrative Cell Biology (I2BC), Paris-Saclay, France. Protein addiction, interaction networks, molecular evolution & engineering, genome integrity
PhD Student | Tonkin-Hill Lab
π¦ Computational Microbiology, Microbiome Metagenomicsπ¦
Solve difficult biological problems using ML/AI.
Cancer Risk Assessment - βCatch Cancer Earlyβ.
Perturbation Biology - computational cell biology - design new combo therapies.
Protein design - function and structure.
News from the Sternberg lab at Columbia University, Howard Hughes Medical Institute.
Posts are from lab members and not Samuel Sternberg unless signed SHS. Posts represent personal views only.
Visit us at www.sternberglab.org
Images, AI, ML, and ALife.
Former: @hampshirecolg
@brandeisuniversity.bsky.social
@harvardmed.bsky.social
@uidaho.bsky.social
@hhmijanelia.bsky.social
@mdc-berlin.bsky.social
@ORNL.
Now @chanzuckerberg.bsky.social.
Opinions are mine.
Scientific Consultant (thomashopf.com)
PhD student@MIT
https://sites.google.com/view/yehlincho/home
Scientist in Comparative Genomics at Institute of Biotechnology, Life Sciences Center, Vilnius University, Lithuania and Guest Researcher at National Center for Biotechnology Information (NCBI), NIH, US
I love large biomedical data.
π https://roman-bushuiev.github.io/
PhD student at CTU Prague working on machine learning for molecule discovery https://anton-bushuiev.github.io
scientist at UC Berkeley inventing advanced genomic technologies
lover of molecules, user of computers
https://scholar.google.com/citations?user=63ZRebIAAAAJ&hl=en
PhD in Arctic Ocean microbial ecology, omics, evolution & diversity. Looking for a postdoc position in Europe. π¦ π§¬βοΈπ©π»βπ»
Also nature/wildlife, mental health, neurodiversity and cats π€Ώππ§ πΊπΏ
French/British/European π«π·π¬π§πͺπΊ
Amaro Lab (UC San Diego), PhD student Biochemistry and Molecular Biophysics | Computational Biology
