⏰ URGENT! ⏰ Into structural modeling, design, integration with experiments, evolution, or platforms? Join our conference, share your work, and see what’s hot! Only 4 days left to submit your abstract! 👇

EMBL Events@events.embl.org · last yr.

Join us at #EMBOComp3D to explore cutting-edge breakthroughs in computational structural biology, AI, drug design, and innovative software! 💻 Find out about molecular modelling to systems-level analyses and evolution, and more. Submit your abstract by 26 Aug ➡️ s.embl.org/csb25-01-bl

Join us at #EMBOComp3D to explore cutting-edge breakthroughs in computational structural biology, AI, drug design, and innovative software! 💻 Find out about molecular modelling to systems-level analyses and evolution, and more. Submit your abstract by 26 Aug ➡️ s.embl.org/csb25-01-bl

One month remaining to register for our conference! Have a look at the outstanding speakers and programme, and use the link to join the 2nd edition of the Computational Structural Biology Conference in Heidelberg!

EMBL Events@events.embl.org · last yr.

Join us at #EMBOComp3D to explore cutting-edge breakthroughs in computational structural biology, AI, drug design, and innovative software! 💻 Find out about molecular modelling to systems-level analyses and evolution, and more. Submit your abstract by 26 Aug ➡️ s.embl.org/csb25-01-bl

New method toward modeling cells and viruses! HMFF enables integrative membrane modeling and simulation guided by electron microscopy data. Created by Valentin Maurer and Marc Siggel @embl.org ‪‪@cssbhamburg.bsky.social‬, in collaboration with @WPezeshkian lab (1/n) www.biorxiv.org/content/10.1...

Are you a postdoc ready for transition to an independent position? You connect infection biology with cutting-edge structural biology or multimodal imaging? Are you aware of such a colleague? I am seeking speakers for "The Next Generation in Infection Biology" microsymposium on June 6 2025.

28 children spent the day at CSSB for Girls' and Boys' Day yesterday! The kids built microscopes, conducted chemistry and chromatography experiments, tried VR goggles and much more. @carobarisch.bsky.social @landaulabcssb.bsky.social @jankosinski.bsky.social @topf-lab.bsky.social

We captured a snapshot of in-cell protein contact sites during influenza A virus infection. In-cell crosslinking, AlphaFold modeling, and functional follow-ups revealed new host factors and mechanisms. A step toward modeling the infected cell.

Sorry Albert, I can't have coffee with you today because time is relative, and mine just ran out. #chatgpt4o

Draw a ribbon representation of a protein structure shaped like a banana, with alpha-helices, beta-sheets, and loops clearly visible, maintaining realistic molecular geometry and coloring styles typical for protein visualizations.

Join us in Heidelberg for the 2nd edition of #EMBOComp3D! 🧬 Explore cutting-edge AI-driven innovations and classical methods in biomolecular research, new sessions on drug design, and make contacts during the job fair. Submit your abstract by 26 Aug 👉 s.embl.org/csb25-01-bl

⏰ You have until 3 March to submit your abstract and be part of #EESInfection ➡️ https://s.embl.org/ees25-04-bl 🦠 🍄 This symposium will bring together researchers working on different pathogens and pave the way for new strategies to overcome current challenges in the treatment of infections 💡

"We demonstrate that current co-folding approaches largely memorise ligand poses from their training data, hindering their use for de novo drug design."

Peter Škrinjar@peterskrinjar.bsky.social · last yr.

Excited to share our latest preprint evaluating AlphaFold3, Boltz-1, Chai-1 and Protenix for predicting protein-ligand interactions, featuring our newly introduced benchmark dataset 🌹Runs N’ Poses🌹! www.biorxiv.org/content/10.1... 🧵👇 (1/n)

PDB-IHM (formerly PDB-Dev) is for integrative structures. Intergrative structures = from multiple experimental & computational methods. Since mid-2024 assigned PDB ids & DOIs. Access via wwPDB archive or PDB-IHM - pdb-ihm.org 👉 https://www.wwpdb.org/news/news?year=2025#677880ea44a8c95814022eb9

The legendary EMBO Integrative Modeling Course is back! If you want to be in this picture in the 2025 edition, just go ahead and register at meetings.embo.org/event/25-bio... Organized by myself & @amjjbonvin.bsky.social & @arneelof.bsky.social & @lindorfflarsen.bsky.social

"Challenges along the way, but it worked out in the end" youtu.be/HnT1VWzdFWc?...

2024 Nobel Prize lectures in chemistry | David Baker, Demis Hassabis and John Jumper

YouTube video by Nobel Prize

youtu.be

Perhaps this is not the only time this picture will be shown during a Nobel Prize lecture 😉

Do you want to work at the interface of molecular simulations, structural biology experiments and #AI? Come to Paris for a PhD at @pasteur.fr 1 PhD position is available in our lab funded by ERC_Research. Please repost!! #compchem #compbio Info 👇 research.pasteur.fr/b/15Hr

Conclusion for ligand session in #casp16, without a template methods fail

Does anyone know of published test cases I can use to evaluate the approach? Ideally, the test case would feature a structure published after 30 September 2021, fail with AlphaFold3, and include real crosslinking data.

@jankosinski.bsky.social · 2y ago

Crosslinks can sometimes improve AlphaFold3 models. Crosslinking is an experimental method often used as a source of distance restraints in modeling. In AlphaFold3, instead of using restraints, crosslinks can be included as covalent ligands. Thanks to Agnieszka Obarska-Kosinska for the idea.

By the way, seeds are your friends when running AlphaFold 3. I use at least 20 by default.

We have released version 2 of AlphaPulldown - a general pipeline for high-throughput structural modeling! Software: github.com/KosinskiLab/... Preprint: biorxiv.org/content/10.1...

Crosslinks can sometimes improve AlphaFold3 models. Crosslinking is an experimental method often used as a source of distance restraints in modeling. In AlphaFold3, instead of using restraints, crosslinks can be included as covalent ligands. Thanks to Agnieszka Obarska-Kosinska for the idea.

Finally on board the Flight towards #casp16. If you want to see my talk you can find it here m.youtube.com/watch?v=w1fG...

CASP16 Lecture - Elofsson

YouTube video by Introduction to Bioinformatics by Arne Elofsson at Stockholm University

m.youtube.com

#casp16 @arneelof.bsky.social @amjjbonvin.bsky.social what is the current state-of-the-art measure for reporting the quality of protein-protein docking models? sequence-dependent interface TM-score? Fnat? I guess not interface RMSD? What tool would you recommend to calculate all of them?

Here is the plot for the protein complex predictions. AlphaFold3 server is an improvement over AlphaFold2 baseline represented by ColabFold. #CASP16

#CASP16 program is posted (so you can guess the "winners". Congratulations to Yang and Kihara who seems to have done well in RNA+Proteins. Also congratulations to AF3-server (i.e. me) who was selected to talk (i.e. most people did worse than the server). predictioncenter.org/casp16/doc/C... .

Really looking forward to welcoming & meeting the participants of our #EMBOStructBio course this morning! Many of our speakers/tutors are here: @moalquraishi.bsky.social @sykhalid.bsky.social @ezgikaraca.bsky.social @amjjbonvin.bsky.social @gchojnowski.bsky.social @drmelissagraewert.bsky.social

UPDATE: Nature.com has issued a correction: “Correction 14 November 2024: An earlier version of this article stated that AlphaFold3 is now ‘open source’. This is not the case, as weights for the model can only be accessed upon request, and the code can only be used for non-commercial applications.”

AI protein-prediction tool AlphaFold3 is now more open

The code underlying the Nobel-prize-winning tool for modelling protein structures can now be downloaded by academics.

nature.com

Hello, I am Jan, and I like molecules and other molecules. Where is a bookmark post button?