Issue 59 | February 2025
BioExcel NEWSLETTER
Dear reader,
In this edition of the BioExcel Newsletter we feature an exciting series of upcoming webinars as well as updates from some of our core software. We highlight some upcoming training events and a recent publication which showcases some impressive GROMACS scaling on CPUs.
The BioExcel Team

BioExcel Webinar series

We have a great line-up of topics and speakers for our webinar series during March and April. Starting next week on 4 March, Tatiana Shugaeva will talk about "Cryo-EM structure refinement with density-guided simulations in GROMACS". Also in March we will hear Elisa Fadda present on "Restoring protein Glycosylation with GlycoShape" and Siewert-Jan Marrink take us through the latest "Perspective on simulating whole cells with Martini". Our first webinar in April features Marco Giulini who has helped develop the HADDOCK3 software discuss "Modelling antibodies in the post-Alphafold era: where are we now?". Additional webinars will be scheduled before the summer so keep checking our website for more information!

BioExcel software development update

GROMACS:

The new version of GROMACS (2025) was released earlier this month. In our recent webinar, Berk Hess takes you through the new features and performance improvements associated with this major release. You can also check out the GROMACS development roadmap for further information on development priorities based on user feedback.

HADDOCK:

Our updated HADDOCK development roadmap shows the recent progress made on implementing new features based on user feedback. Coarse-graining support based on the Martini force field, improved support for protein-glycan modelling and modelling of anti/nanobody complexes is being worked on. You can follow these developments in the official HADDOCK GitHub repository.

BioExcel Building Blocks (BioBB):

BioBB modules are now included as plug-ins in the Horus workflow manager; "Horus is a free to use multi-platform workflow manager which allows developers and scientists to create, manage and execute complex workflows related to biomolecular modeling or other scientific fields".

Ambassador Program workshop: May 2025 in Sofia, Bulgaria

As part of our Ambassador Program and in collaboration with our colleagues at the National Competence Centres for HPC in Bulgaria, Romania, Serbia and North Macedonia we are organising a workshop from 21 to 22 May 2025 in Sofia, Bulgaria. The workshop will cover the use of some of the core BioExcel software codes. Registration will open soon and you can find further information on our website.

Publication: Scaling GROMACS on CPUs

Recent work supported by BioExcel demonstrates near-perfect scaling of highly optimised GROMACS simulations containing up to 200 million atoms on a High Performance Computing (HPC) cluster consisting of over 65,000 CPU cores. This work demonstrates that we are in a position to effectively simulate viruses, organelles and, soon, small cells using modern HPC machines. Read all about it in the publication by Kutzner et al. (2025).

EMBO Practical Course: Integrative modelling of biomolecular interactions

If you are interested in a hands-on learning experience covering computational approaches and recent AI developments for predicting how proteins interact with other biomolecules or ligands, then look no further than the EMBO Practical Course on Integrative Modelling of Biomolecular Interactions to be held in Izmir, Turkey from 28 September to 3 October 2025. Registration deadline is 15 June 2025.

Request: please acknowledge BioExcel support

We are passionate about providing high quality support to users of our codes and have done so for many years. We have a small favour to ask those who have received this support and read this message.
Please take a moment to acknowledge the BioExcel Centre of Excellence as part of your dissemination through journals, presentations or other forms of communication. It would mean the world to us! Further, we would be delighted if you could drop us a quick email at team@bioexcel.eu to let us know how we have helped you. Thank you for your continued support!
We handle your data responsibly and we don't share it with third parties. Find out more about our Privacy Policy. You may unsubscribe at any time but we hope you will stay in touch.
Unsubscribe | Manage subscription