BioExcel CoE

👏 Congratulations to the Summer School 2025 poster prize winners!

🏆 Zuzana Janáčková
🏆 Jan van Elteren
🏆 Gesa Laura Freimann

Join us for a special edition webinar where they will present their work

🗓️ 23 September 2025, 15:00 CET

Today was the last day of our Summer School on Biomolecular Simulations 2025 ☀ 🏖

Finishing off with an introduction to QM/MM by Emiliano Ippoliti and a 'careers session' for all participants

Thank you to everyone for a great event 👋

During the afternoon session we were joined online by Sergey Ovchinnikov who gave some invaluable insights into #alphafold

Sergey talked about AlphaFold3 and its limitations. If you are looking for alternatives, check out ColabFold ➡ bit.ly/3KQEHOe

@sokrypton.org

Webinar: Using interactive Jupyter Notebooks and BioConda for FAIR and reproducible biomolecular simulation workflows (2024-05-28) View slides on Zenodo Abstract Interactive Jupyter Notebooks in combination with Conda environments can be used to generate FAIR (Findable, Accessible, Interoperable and Reusable/Reproducible) biomole...

As more scientific journals are starting to require reproducibility before publication #BioBB can become invaluable

Check out our #webinar on BioBB and #FAIR workflows ➡️ bit.ly/3xXBcCm

The tutorial uses #GROMACS as the simulation engine. Find this and other #workflow examples here ➡ bit.ly/3xzZJ0q

#BioBB enables automated system preparation, simulation and analysis, making your workflows and environment reproducible and #FAIR

Day 4 of the Summer School 2025 was about workflows and protein structure prediction

Adam Hospital introduced BioExcel Building Blocks #BioBB and followed up with a hands-on #tutorial on how to perform protein-ligand complex #moleculardynamics in Jupyter notebooks using BioBB

Sudarshan Behera gave an intro to free energy calculations followed by a #tutorial on using #pmx and #GROMACS to set up a ligand-binding relative free energy calculation study

Access the tutorial ➡ bit.ly/45Bcp3V and a #webinar on the topic ➡ bit.ly/3XjSJxf 📹

@sudars.bsky.social

This was illustrated during the hands-on session on calculating the potential of mean force (PMF) along a reaction coordinate using the AWH method in #GROMACS

Find the #tutorial here ➡ bit.ly/4c8xeWG and our #webinar on its application ➡ bit.ly/3xqERbY 📽️

Day 3 of the Summer School is about enhanced sampling and free energy calculations⚡️

Berk Hess introduced the AWH method implemented in #GROMACS and illustrated its application to alchemical transformations where the main challenge is to define a good reaction coordinate

An engaging tutorial by Attilio, Giuliano Malloci and Mohd Athar enabled participants to test the #EDESmethod for enhanced sampling ➡ bit.ly/45Rdp3h

Attilio Vargiu gave an in-depth lecture on biomolecular recognition and enhanced sampling methods, covering techniques like Replica Exchange MD, Metadynamics, Accelerated MD, Targeted MD, and more, illustrated with multiple case studies

Anna Kravchenko took participants through the HADDOCK3 tutorial for antibody-antigen modeling

This tutorial and other useful learnings including how to carry out antibody-antigen structure prediction from sequence using #alphafold can be found here ➡ bit.ly/45LCWgY

Day 2 of the Summer School is about molecular recognition and docking 🤝

@amjjbonvin.bsky.social introduces #HADDOCK to predict interactions between: proteins, nucleic acids, glycans and small molecules

For further flexibility and customisation check out HADDOCK3 ➡️bit.ly/4mQLZn7

First full day of the Summer School on Biomolecular Simulations 2025 in Sardinia 😎 🏖️

It's mostly about #moleculardynamics and #GROMACS with lectures and hands-on tutorials

Check out these useful MD tricks from Prof. Berk Hess👇

Get inside a bacterial cell with this cool combination of @cg-martini.bsky.social and @viamd.bsky.social

Also check out our recent webinars on each:

🎬 Whole cell simulation with Martini ▶️ youtu.be/fvFaPgSoM90

🎬 Visual analysis of #moleculardynamics with VIAMD ▶️ youtu.be/wVENzcx0XmQ

@fabioaffinito.bsky.social there don't seem to be any issues our end. Are you still unable to access?

Registration for the Martini workshop, 11-15 August 2025 in Groningen, is now open!

Learn from the cocktail masters themselves how to prepare your optimal Martini simulations, making use of the latest tools.

Info and application: cgmartini.nl
Deadline: 15 June

Read about the recent #compchem Spring School held @csc.fi and 🔑 access the training materials

➡️bioexcel.eu/rj58

✅ Classical #moleculardynamics
✅ Electronic structure theory
✅ #machinelearning in chemistry
✅ Enhanced sampling methods

#quantumchemistry #AI

Our webinar series will restart in September 2025 following a break during the summer months ☀️⛱️

📽️ You can access the recordings of all our previous webinars via our YouTube channel ▶️ bit.ly/3H8FZW7

#molecularmodeling #molecularsimulations #research #compchem

Join us today 13th May at 15:00 CET for our last webinar before the summer break 😎

"MiMiC: A high-performance framework for multiscale molecular dynamics simulations"
Registration ➡️ bioexcel.eu/l4rd

#moleculardynamics #qmmm #compchem

A great opportunity to work with the GROMACS development team in Sweden on enhanced sampling in molecular dynamics🔝🖥️🇸🇪

ℹ️ More information: bioexcel.eu/u583
🗓️ Application deadline: 2 June 2025

#jobs #moleculardynamics

The manuscript describing the new modular version of HADDOCK is finally available as a preprint! The result of a team work over several years, supported by @bioexcelcoe.bsky.social @bijvoet-centre.bsky.social @esciencecenter.bsky.social - www.biorxiv.org/content/10.1...

Our webinar on "MiMiC: A high-performance framework for multiscale molecular dynamics simulations" is next week on Tuesday 13 May at 15:00 CET

Don't forget to register ➡️ bioexcel.eu/l4rd

#moleculardynamics #qmmm #compchem

Last day of this year's Computational Chemistry Spring School held @CSCfi

✅Classic #moleculardynamics
✅Electronic structure theory
✅#AI in chemistry
✅Hands-on tutorials running on supercomputer GPUs
✅Poster session & networking

🌍24 participants / 8 countries

#compchem

Webinar: MiMiC: A high-performance framework for multiscale molecular dynamics simulations (2025-5-13) Date: 13 May 2025 Time: 15:00 CEST Registration   Abstract These days, computational chemists can choose from a wide variety of software packages, each with its own unique features and strengths. Man...

Join us for our next webinar where Andrej Antalík will introduce the MiMiC framework for multiscale modeling in computational chemistry

🗓️ 13 May 2025, 15:00 CET
✍️ Sign up: bioexcel.eu/l4rd

#moleculardynamics #qmmm #compchem

Registration for our hybrid workshop closes on 15 April 2025 ‼️

Note the registration requirements before submitting your application ➡️ bioexcel.eu/sl42

#GROMACS #HADDOCK #PMX #software

@eurocc.bsky.social @euroccbg.bsky.social

🔜 Join us tomorrow at 15:00 CET (UTC+1) to hear about "Modelling antibodies in the post-Alphafold era: where are we now?"

Registration is still open ➡️ bit.ly/4bYUozP

#webinar #antibody #AlphaFold #proteindesign #compchem

Our webinar "Modelling antibodies in the post-Alphafold era: where are we now?" is next week on Tuesday 8 April at 15:00 CET

Don't forget to register ➡️ bit.ly/4bYUozP

#antibody #HADDOCK #AlphaFold #proteindesign #compchem
@amjjbonvin.bsky.social

Interested in an entry-level, hands-on workshop on #GROMACS, #HADDOCK and #PMX software?

Look no further than our Ambassador Program event:

🗓️ 21-22 May 2025
🌍 Sofia, Bulgaria & online
Info ➡️ bioexcel.eu/sl42

➕EuroCCs Bulgaria, Montenegro, North Macedonia, Romania, Serbia

@euroccbg.bsky.social

Webinar: Modelling antibodies in the post-Alphafold era: where are we now? (2025-4-8) Date: 8 April 2025 Time: 15:00 CET Registration Abstract Antibodies are specialized proteins used by the immune system to eliminate unrecognized, potentially harmful molecules (antigens). Their abili...

Interested in #antibody modelling?

Marco Giulini will discuss the current state of antibody modelling in the post-AlphaFold era in our next webinar:

🗓️ 8 April 2025 (15:00 CET)
✍️ bit.ly/4bYUozP

#HADDOCK #AlphaFold #proteindesign #compchem