Alexandre Bonvin
@amjjbonvin.bsky.social
Reposted by 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
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
November 12, 2025 at 12:35 PM
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
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
Reposted by Alexandre Bonvin
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...
www.uu.nl/en/news/33-m...
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...
www.uu.nl
November 4, 2025 at 7:14 AM
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...
www.uu.nl/en/news/33-m...
Looking forward to contribute!
I attended a summer school on Spetses 🇬🇷 just as I was beginning my PhD. Looks like I will be going again in 2026 with "Lost in Integration vol. 2". Details to follow.
October 29, 2025 at 7:31 AM
Looking forward to contribute!
Reposted by Alexandre Bonvin
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...
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
github.com
October 28, 2025 at 9:30 AM
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...
Reposted by Alexandre Bonvin
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
Learn more here: buff.ly/gInH6VV
#SBGrid #SBGridSoftware #StructuralBiology
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…
buff.ly
October 24, 2025 at 4:08 PM
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
Learn more here: buff.ly/gInH6VV
#SBGrid #SBGridSoftware #StructuralBiology
Reposted by Alexandre Bonvin
AbTune: Layer-wise selective fine-tuning of protein language models for antibodies https://www.biorxiv.org/content/10.1101/2025.10.17.682998v1
October 18, 2025 at 12:47 AM
AbTune: Layer-wise selective fine-tuning of protein language models for antibodies https://www.biorxiv.org/content/10.1101/2025.10.17.682998v1
Reposted by Alexandre Bonvin
🧬 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
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
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...
onlinelibrary.wiley.com
October 6, 2025 at 11:47 AM
🧬 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
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.
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.
October 9, 2025 at 9:37 AM
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.
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.
Reposted by Alexandre Bonvin
And the legacy continues! 😊
@amjjbonvin.bsky.social @bioinfo.se @lindorfflarsen.bsky.social #EMBOIntegMod25 ! 🍀🧿
@amjjbonvin.bsky.social @bioinfo.se @lindorfflarsen.bsky.social #EMBOIntegMod25 ! 🍀🧿
October 6, 2025 at 1:13 PM
And the legacy continues! 😊
@amjjbonvin.bsky.social @bioinfo.se @lindorfflarsen.bsky.social #EMBOIntegMod25 ! 🍀🧿
@amjjbonvin.bsky.social @bioinfo.se @lindorfflarsen.bsky.social #EMBOIntegMod25 ! 🍀🧿
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.
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...
www.linkedin.com
September 24, 2025 at 1:30 PM
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.
Reposted by Alexandre Bonvin
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...
The European Bioinformatics Institute < EMBL-EBI
EMBL-EBI
www.ebi.ac.uk
September 19, 2025 at 9:35 PM
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...
Reposted by Alexandre Bonvin
Navigating the pre- and post-AlphaFold divide: CAPRI 8th evaluation meeting
www.authorea.com/users/348903...
www.authorea.com/users/348903...
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 ...
www.authorea.com
September 15, 2025 at 3:36 PM
Navigating the pre- and post-AlphaFold divide: CAPRI 8th evaluation meeting
www.authorea.com/users/348903...
www.authorea.com/users/348903...
Reposted by Alexandre Bonvin
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
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
September 12, 2025 at 3:17 PM
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
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
Reposted by Alexandre Bonvin
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
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
September 12, 2025 at 6:22 AM
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
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
Reposted by Alexandre Bonvin
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
Through a combination of AlphaFold2 and other tools we are bypassing the limits of traditional MD simulations ➡️ bioexcel.eu/dvy3
#Proteins #MolecularDynamics #GROMACS #AlphaFold2
September 9, 2025 at 8:04 PM
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
Through a combination of AlphaFold2 and other tools we are bypassing the limits of traditional MD simulations ➡️ bioexcel.eu/dvy3
#Proteins #MolecularDynamics #GROMACS #AlphaFold2
Reposted by Alexandre Bonvin
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
⬇️⬇️⬇️
@sib.swiss @biozentrum.unibas.ch
⬇️⬇️⬇️
🔬 Workshop: Future of Structure Prediction Benchmarking
📅 Sept 8, 2025 | Basel
💡 Talks + breakout sessions on #CASP #CAPRI #CAMEO & benchmarking for drug discovery
🎟️ Free registration (limited spots): lu.ma/ws9nu1xf
Join us to explore how benchmarking can drive breakthroughs in structure prediction.
📅 Sept 8, 2025 | Basel
💡 Talks + breakout sessions on #CASP #CAPRI #CAMEO & benchmarking for drug discovery
🎟️ Free registration (limited spots): lu.ma/ws9nu1xf
Join us to explore how benchmarking can drive breakthroughs in structure prediction.
The future of structure prediction benchmarking: measuring progress and breakthroughs · Luma
Benchmarking has been a key driver of progress in protein structure prediction methods. As the field continues to evolve, several key questions prevail:
How…
lu.ma
August 27, 2025 at 5:32 PM
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
⬇️⬇️⬇️
@sib.swiss @biozentrum.unibas.ch
⬇️⬇️⬇️
Reposted by Alexandre Bonvin
this seems like a very good idea actually
August 15, 2025 at 1:38 PM
this seems like a very good idea actually
Reposted by Alexandre Bonvin
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 🧲
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.
www.egi.eu
July 31, 2025 at 5:26 PM
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 🧲
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/
CAPRI Docking
www.capri-docking.org
July 29, 2025 at 6:26 AM
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/
Reposted by Alexandre Bonvin
💻 Code and input data are openly available with documentation and examples to support reproducible antibody modelling and docking workflows:
GitHub - haddocking/alphaflow-antibodies
Contribute to haddocking/alphaflow-antibodies development by creating an account on GitHub.
github.com
July 28, 2025 at 11:01 AM
💻 Code and input data are openly available with documentation and examples to support reproducible antibody modelling and docking workflows:
Reposted by Alexandre Bonvin
🧬 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
Full article available: https://doi.org/10.1093/bioadv/vbaf161
Authors include: @xiaotong-xu.bsky.social, @amjjbonvin.bsky.social
July 28, 2025 at 11:01 AM
🧬 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
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!
Combining AI structure prediction and integrative modelling for nanobody-antigen complexes https://www.biorxiv.org/content/10.1101/2025.07.01.662355v1
July 14, 2025 at 3:12 PM
The result of a master student project by Miguel Sanchez-Marin supervised by Marco Giulini - well done both!
Reposted by Alexandre Bonvin
Biomolecular interaction prediction in the pre and post alphafold era
onlinelibrary.wiley.com/doi/10.1002/...
onlinelibrary.wiley.com/doi/10.1002/...
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...
onlinelibrary.wiley.com
July 14, 2025 at 9:01 AM
Biomolecular interaction prediction in the pre and post alphafold era
onlinelibrary.wiley.com/doi/10.1002/...
onlinelibrary.wiley.com/doi/10.1002/...
Reposted by Alexandre Bonvin
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...
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...
bioexcel.eu
June 26, 2025 at 4:03 PM
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...
Reposted by Alexandre Bonvin
🎶 Science meets creativity with TuberKiller! Yaëlle Wormser, PhD student featured in the My PhD at the Institut Pasteur series, raps her tuberculosis research.
Discover how music and science collide to make research unforgettable! 👏
🎧 TuberKiller is also available on Spotify!
@pasteur.fr
Discover how music and science collide to make research unforgettable! 👏
🎧 TuberKiller is also available on Spotify!
@pasteur.fr
When science meets creativity: TuberKiller | My PhD at the Institut Pasteur
YouTube video by Institut Pasteur EDUCATION
youtube.com
June 20, 2025 at 8:30 AM
🎶 Science meets creativity with TuberKiller! Yaëlle Wormser, PhD student featured in the My PhD at the Institut Pasteur series, raps her tuberculosis research.
Discover how music and science collide to make research unforgettable! 👏
🎧 TuberKiller is also available on Spotify!
@pasteur.fr
Discover how music and science collide to make research unforgettable! 👏
🎧 TuberKiller is also available on Spotify!
@pasteur.fr