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.
π www.science.org/doi/10.1126/...
π search.foldseek.com/foldmason
πΎ github.com/steineggerla...
30.01.2026 06:11 β π 297 π 147 π¬ 4 π 3
A tripartite protein complex promotes DNA transport during natural transformation in Firmicutes | PNAS
Natural genetic transformation is a conserved mechanism of bacterial horizontal gene
transfer, which is directed entirely by the recipient cell and...
Pleased to share our recent article in PNAS - a collaboration with @jessicaandreani.bsky.social & Pablo Radicella, with important roles played by many members of each team.
A tripartite protein complex promotes DNA transport during natural transformation in Firmicutes www.pnas.org/doi/10.1073/...
26.11.2025 07:44 β π 37 π 15 π¬ 2 π 3
New paper alert π¨
I am super happy about it, for many reasons!
π₯ It was a great collaborative project with Calum @chgjohnston.bsky.social and J. Pablo Radicella, designed a long time ago (in the pre-AlphaFold era - can you imagine?) together with @polardlab.bsky.social and @raphguerois.bsky.social
28.11.2025 09:39 β π 10 π 6 π¬ 1 π 0
How do new centromeres evolve while staying compatible with the division machinery?
Discover it in our new Nature paper! We show centromeres transition gradually via a mix of drift, selection, and sex, reaching new states that still work with the kinetochore.
π doi.org/10.1038/s41586-025-09779-1
26.11.2025 16:21 β π 184 π 84 π¬ 8 π 8
Structural basis for fork reversal and RAD51 regulation by the SCF ubiquitin ligase complex of F-box helicase 1 pubmed.ncbi.nlm.nih.gov/41256537/ #cryoEM
21.11.2025 01:10 β π 2 π 2 π¬ 0 π 0
Proteome-wide in silico screening for human protein-protein interactions
Protein-protein interactions (PPIs) drive virtually all biological processes, yet most PPIs have not been identified and even more remain structurally unresolved. We developed a two-step computational...
Thrilled to share that the final piece of my PhD work is now on bioRxiv! biorxiv.org/content/10.1... With support from @nvidia and the @NSF, we used AlphaFold to screen 1.6M+ protein pairs, revealing thousands of potential novel PPIs. All data can be viewed at predictomes.org/hp
12.11.2025 21:26 β π 163 π 67 π¬ 5 π 4
Among the anti-recombinases, FIGNL1 rules them all. So much that inactivating it brings BRCA2-deficient cells to life. Who is responsible for RAD51 loading without BRCA2/FIGNL1, check out the paper to find out! Great collaboration with @raychaudhurilab.bsky.social
www.science.org/doi/10.1126/...
30.10.2025 20:41 β π 53 π 22 π¬ 6 π 1
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
Super excited about first Shendure/Baker Lab collaboration & preprint on a multiplex sequencing-based strategy for screening de novo proteome editors in mammalian cells. Kudos to the brilliant Chase Suiter (not here) & @greenahn.bsky.social on the work! Preprint here:
www.biorxiv.org/content/10.1...
14.10.2025 18:44 β π 97 π 33 π¬ 0 π 0
Thrilled to announce our new preprint, βProtein Hunter: Exploiting Structure Hallucination within Diffusion for Protein Design,β in collaboration with @Griffin, @GBhardwaj8 and @sokrypton.org
π§¬Code and notebooks will be released by the end of this week.
π§Golden- Kpop Demon Hunters
13.10.2025 15:45 β π 53 π 16 π¬ 3 π 2
Exciting to see our protein binder design pipeline BindCraft published in its final form in @Nature ! This has been an amazing collaborative effort with Lennart, Christian, @sokrypton.org, Bruno and many other amazing lab members and collaborators.
www.nature.com/articles/s41...
27.08.2025 16:14 β π 305 π 109 π¬ 14 π 11
π
05.08.2025 21:10 β π 0 π 0 π¬ 0 π 0
Folddisco finds similar (dis)continuous 3D motifs in large protein structure databases. Its efficient index enables fast uncharacterized active site annotation, protein conformational state analysis and PPI interface comparison. 1/9π§Άπ§¬
π www.biorxiv.org/content/10.1...
π search.foldseek.com/folddisco
07.07.2025 08:21 β π 152 π 70 π¬ 8 π 3
AI just cracked de novo antibody design with a 100x leap! π§ͺ
Chai-2, a next-gen multimodal generative model, is shaking up protein design. With a 16% hit rate in fully de novo antibody designβover 100 times better than previous methodsβitβs making drug discovery faster and more precise than ever.
01.07.2025 02:34 β π 19 π 5 π¬ 1 π 2
Excited to unveil Boltz-2, our new model capable not only of predicting structures but also binding affinities! Boltz-2 is the first AI model to approach the performance of FEP simulations while being more than 1000x faster! All open-sourced under MIT license! A threadβ¦ π€π
06.06.2025 13:46 β π 215 π 91 π¬ 10 π 11
π Excited to release BoltzDesign1!
β¨ Now with LogMD-based trajectory visualization.
π Demo: rcsb.ai/ff9c2b1ee8
Feedback & collabs welcome! π
π: GitHub: github.com/yehlincho/Bo...
π: Colab: colab.research.google.com/github/yehli...
@sokrypton.org @martinpacesa.bsky.social
03.06.2025 01:30 β π 54 π 17 π¬ 1 π 0
@science.org π§«π§¬βοΈπ¬ Molecular basis of influenza ribonucleoprotein complex assembly and processive RNA synthesis | Science www.science.org/doi/10.1126/...
@yiweichang.bsky.social www.yiweichanglab.org @jiwasa.bsky.social #virology #Influenza #Cryo-EM #StructuralBiology #RNA #polymerase
15.05.2025 23:11 β π 90 π 21 π¬ 3 π 3
Please see our latest paper on the role of EXO1 in meiosis: "EXO1 promotes the meiotic MLH1-MLH3 endonuclease through conserved interactions with MLH1, MSH4 and DNA". Congratulations to both first authors, Megha Roy and Aurore Sanchez and thanks to all our collaborators!
05.05.2025 07:22 β π 44 π 11 π¬ 0 π 0
DprA recruits ComM to facilitate recombination during natural transformation in Gram-negative bacteria | PNAS
Natural transformation (NT) represents one of the major modes of horizontal gene transfer
in bacterial species. During NT, cells can take up free D...
π£ Happy to announce that "DprA recruits ComM to facilitate recombination during natural transformation in Gram-negative bacteria" just got published in PNAS www.pnas.org/doi/abs/10.1...
π§¬π§Άπ©βπ¬π©βπ» Collaborative and interdisciplinary work, together with the groups of Ankur Dalia and J. Pablo Radicella
14.04.2025 05:42 β π 13 π 5 π¬ 1 π 0
𧬠@science.org Structural insights into chromatin remodeling by ISWI during active ATP hydrolysis | Science www.science.org/doi/10.1126/...
14.04.2025 05:04 β π 13 π 2 π¬ 1 π 0
I am a professor at Columbia University. All of the student NIH training grants have been canceled and now there are reports that ALL funding will be frozen. Why are Universities not banding together and speaking out publicly and forcibly about governmental attacks on biomedical research?
11.04.2025 16:53 β π 1308 π 408 π¬ 53 π 19
Probabilistic machine learning to address questions in evolution and health #EvolutionaryMedicine. PI at the Centre for Genomic Regulation, co-leading a group with Mafalda Dias. Previously Harvard.
PhD student @mit.edu, previously @deshawresearch.com, @harvard.edu
CNRS researcher in the pneumococcal competence and transformation team in Toulouse.
Using molecular genetics and cell biology to study pneumococcal competence and transformation.
Incoming PI at Institut Pasteur π«π·
Current: Evolutionary Virologist based at the University of Tokyo π―π΅
π»π¦ π³οΈβπ
Full stack developer who occasionally wears a lab coat. Currently a machine learning researcher at Manifold Bio.
Unofficial account exploring the intersection of biology, molecules, science, AI and protein folding with AlphaFold.
Group leader at I2BC - Paris-Saclay. de novo genes & microproteins | structure & evolution http://bim.i2bc.paris-saclay.fr/anne-lopes
Structural & Systems Biology Lab @ University of Geneva | Exploring protein & proteome assemblies | Structured thoughts, intrinsically disordered views
Open source #bioinformatics at Sungkyunkwan University π°π· | former Steinegger Lab @ SNU, SΓΆding Lab @ MPI-NAT | http://mstdn.science/@milotmirdita
MIT PhD Student - ML for biomolecules - https://hannes-stark.com/
Virus origins/diversity/evolution; mobilome; Archaea.
Head of the Cell Biology and Virology of Archaea Unit at Institut Pasteur:
https://research.pasteur.fr/en/team/archaeal-virology/
Group leader at I2BC | EVOGEN team | Evolutionary geneticist interested in intragenomic conflicts and genome evolution.
Evolutionary systems/cell biologist. EMBO and SNSF Postdoctoral Fellow with Dmitri Petrov and Dan Jarosz at Stanford. PhD with Andreas Wagner at the University of Zurich. Studying how molecular and cellular systems shape, and are shaped by, evolution.
PhD researcher @ University of Copenhagen & Gubra
Machine Learning for design and optimization of peptide therapeutics
PhD student@MIT
https://sites.google.com/view/yehlincho/home
Group Leader at Institute of Molecular Biology, Mainz, Germany
The Sorek Lab
Weizmann Institute of Science, Israel
https://www.weizmann.ac.il/molgen/Sorek/
Associate professor at ETH Zurich, studying the cellular consequences of genetic variation. Affiliated with the Swiss Institute of Bioinformatics and a part of the LOOP Zurich.
