Alexandre Bonvin

Join us for our next #webinar where we will provide an overview of the #GROMACS Tutorials Suite

We will cover different methods and installation of all the necessary software requirements

🗓️ 2 December 2025, 15:00 CET
✍️ bioexcel.eu/4m5m

#moleculardynamics #freeenergy #enhancedsampling

33 million euro investment for national electron microscope facility EMPower A major new national facility for electron microscopy, called EMPower, has been awarded to a consortium of Dutch universities and medical centers. EMPower aims to pave the way for major discoveries im...

Very happy that NWO supports this major upgrade of our national EM infrastructure. It is great that this initiative got broad support all over NL, and it will EMPower fantastic science - looking forward to that!
www.uu.nl/en/news/33-m...

Looking forward to contribute!

GitHub - aqlaboratory/openfold-3: OpenFold3: A fully open source biomolecular structure prediction model based on AlphaFold3 OpenFold3: A fully open source biomolecular structure prediction model based on AlphaFold3 - aqlaboratory/openfold-3

Looks like OpenFold3 has been formally released in a public "preview". Not quite on parity with AlphaFold3 on a few benchmarks shown, in particular for antibody interactions. All info on the github link. I am sure we will hear more about this from the developers github.com/aqlaboratory...

A brief introduction to HADDOCK3 — haddock3 3.0.0 documentation HADDOCK3 is the next generation integrative modelling software in the long-lasting HADDOCK project. It represents a complete rethinking and rewriting of the HADDOCK2.X series, implementing a new way…

New Title Alert: HADDOCK3- is the next generation integrative modeling software in the long-lasting HADDOCK project.

Learn more here: buff.ly/gInH6VV

#SBGrid #SBGridSoftware #StructuralBiology

AbTune: Layer-wise selective fine-tuning of protein language models for antibodies https://www.biorxiv.org/content/10.1101/2025.10.17.682998v1

Biomolecular Interaction Prediction in the Pre‐ and Post‐AlphaFold Era: The 8th CAPRI Evaluation We report on the 8th CAPRI Evaluation period, capturing the assessment of CAPRI Rounds 47 to 55 (excluding the CASP and COVID-related Rounds), which have witnessed the transition to AI-driven predict...

🧬 New paper out from our Computational Molecular Systems Biology team at @UGSF-lille !
Proud to have contributed to the CAPRI 8 challenge

🔗 Read it here: onlinelibrary.wiley.com/doi/10.1002/...

#CAPRI8 #AlphaFold #ProteinStructure #StructuralBiology #AIinBiology #Bioinformatics #UGSF

INTERNATIONAL SYMPOSIUM ON GRIDS & CLOUDS (ISG) 2026
15-20 March 2026, Academia Sinica, Taipei, Taiwan

CALL FOR ABSTRACT

There will also be a #HADDOCK @bioexcelcoe.bsky.social workshop in the context of the EU-INDIA GANANA project.

And the legacy continues! 😊

@amjjbonvin.bsky.social @bioinfo.se @lindorfflarsen.bsky.social #EMBOIntegMod25 ! 🍀🧿

Almost on my way - Needed first to finish the second batch of “vendanges” 😀 see you soon!

Announcing CAPRI round 61 with four antibody-antigen targets - registration is open and the prediction period starts on Monday September 29th. Put your methods to the test! Visit… | Alexandre Bonvin Announcing CAPRI round 61 with four antibody-antigen targets - registration is open and the prediction period starts on Monday September 29th. Put your methods to the test! Visit https://lnkd.in/ei68T...

Still time to register for the next CAPRI round and put your methods to the test for predicting the structure of four antibody-antigen complexes - prediction period opening on Sept. 29th.

A new CAPRI round is coming up with 4 antibody-antigen targets! The registration opens next Monday (Sept. 22nd). Check it out at www.ebi.ac.uk/pdbe/complex...

Navigating the Pre- and Post-AlphaFold Divide: CAPRI 8th evaluation meeting, February 12-14, Grenoble, FR Navigating the Pre- and Post-AlphaFold Divide: CAPRI 8th evaluation meeting, February 12-14, Grenoble, FRAlexandre M.J.J. Bonvin1 and M. F. Lensink21 Bijvoet Centre for Biomolecular Research, Faculty ...

Navigating the pre- and post-AlphaFold divide: CAPRI 8th evaluation meeting

www.authorea.com/users/348903...

5️⃣ Featuring the fifth of our showcase projects

Our automated pipeline, built on BioBBs, uses #AlphaFold, MD simulations, and virtual screening to output a list of ligand poses ➡️ bioexcel.eu/1c1j

#DrugDiscovery #Workflows #CADD #VirtualScreening

4️⃣ Featuring the fourth of our showcase projects

Upgrading GROMACS to handle billion-atom systems and enhancing I/O performance and precision, making the first-ever whole-cell simulation possible ➡️ bioexcel.eu/uw67

#MolecularDynamics #GROMACS #ComputationalBiology

2⃣ Featuring the second of our showcase projects

Through a combination of AlphaFold2 and other tools we are bypassing the limits of traditional MD simulations ➡️ bioexcel.eu/dvy3

#Proteins #MolecularDynamics #GROMACS #AlphaFold2

Cafaggi! 😋

Critical benchmarking of structure prediction methods has been crucial for measuring progress and detecting breakthroughs. But how will the future look like? Join the discussion at our workshop in Basel on September 8 - just before the [BC]2 conference.

@sib.swiss @biozentrum.unibas.ch

⬇️⬇️⬇️

reddit screenshot r/technology 70 people here Al's Biggest Threat: Young People W... 4.3k upvotes • 442 comments SonofRodney • 6h I recently heard about a teacher who instead of trying to circumvent students using ai, which is impossible, she made assignments by going "ask ChatGPT to write a report on this subject, and then research how and why it's wrong". Not only did the students discover that chatGPT is extremely wrong a lot of the time, it also lead them to realize that they should not use it as a primary source.

this seems like a very good idea actually

Empowering Structural Biology: Inside WeNMR’s Journey with EGI Now serving over 66,000 users in 174 countries, WeNMR’s success is built on user-friendly tools like the HADDOCK server, strong support and training, and a commitment to scientific excellence.

Alexandre Bonvin @amjjbonvin.bsky.social Empowering Structural Biology: Inside WeNMR’s Journey with EGI (European Grid Infrastructure) EGI Magazine - Issue 03 @egieinfra.bsky.social www.egi.eu/magazine/iss... #NMRchat #NMR 🧲

Rounds are organised whenever we get a target. Very different from CASP. Sometimes the schedule is tight because of a publication coming out soon

We are surely interested in those! Had a few targets in the past

Blind structure prediction experiments like CASP and CAPRI are catalysts of new developments

CAPRI Docking

A small reminder to all structural biologists around working on biomolecular complexes: please consider sharing your complexes as targets for CAPRI - AI has not solved all structure prediction problems and there are still challenges! See www.capri-docking.org/contribute/

GitHub - haddocking/alphaflow-antibodies Contribute to haddocking/alphaflow-antibodies development by creating an account on GitHub.

💻 Code and input data are openly available with documentation and examples to support reproducible antibody modelling and docking workflows:

🧬 Now published in Bioinformatics Advances: "Improved prediction of antibody and their complexes with clustered generative modelling ensembles"  

Full article available: https://doi.org/10.1093/bioadv/vbaf161

Authors include: @xiaotong-xu.bsky.social, @amjjbonvin.bsky.social

The result of a master student project by Miguel Sanchez-Marin supervised by Marco Giulini - well done both!

Biomolecular Interaction Prediction in the Pre‐ and Post‐AlphaFold Era: The 8th CAPRI Evaluation We report on the 8th CAPRI Evaluation period, capturing the assessment of CAPRI Rounds 47 to 55 (excluding the CASP and COVID-related Rounds), which have witnessed the transition to AI-driven predict...

Biomolecular interaction prediction in the pre and post alphafold era

onlinelibrary.wiley.com/doi/10.1002/...

Cheers to that (completing one week of farniente on Elba 😎)

Featured Ambassador: Vlad Cojocaru About Vlad Cojocaru was born in Arad, a city located at the western border of Romania and is a leading scientist in the field of computational biochemistry. His scientific career started when he met T...

Very honored to feature on the @bioexcelcoe.bsky.social Newsletter as one of the ambassadors of the month together with Anela Ivanova for co-organizing the Bioexcel Balkan Workshop in May in Sofia. BioExcel links a very friendly and impactful community. bioexcel.eu/about/govern...