Issue 60 | April 2025
BioExcel NEWSLETTER
Dear reader,

In this edition of the BioExcel Newsletter we include updates from some of our core software as well as a success story featuring the use of HADDOCK in drug discovery. We kick-off our 'Ambassador of the month' feature and highlight some recent publications and our upcoming webinar on the MiMiC framework for multiscale modeling in computational chemistry.

The BioExcel Team

BioExcel software development update

GROMACS:

Following the release of the new version of GROMACS (2025) in February you can follow the development priorities and implemented features via the GROMACS development roadmap.

HADDOCK:

Check out the first version of the HADDOCK3 user guide. Your feedback is welcome!
You can follow our ongoing efforts to bring additional features and further develop HADDOCK through our HADDOCK development roadmap and the HADDOCK GitHub repository.

BioExcel Building Blocks (BioBB):

Use of BioBB FAIR workflows and the OpenOnDemand platform enabled participants at the recent EuroCC/BioExcel workshop in Istambul to run different workflows in JupyterLab and through the command line without the need for further installations.
Check out the BioBB development roadmap for an up-to-date view of all the recent development priorities based on user feedback such as new or updated building blocks for GROMACS, HADDOCK and PMX or new building blocks for, e.g. enhanced sampling, structural conformation prediction or QM methods.

Impact: the long path to therapeutic antibodies

Its not often that we get visibility of the impact we have on the design of approved therapeutics. In this short article we describe how the HADDOCK software was used to help design a now FDA-approved therapeutic to treat certain types of cancer.

BioExcel webinar

Our next webinar is on the 13 May at 15:00 CET and will be presented by Andrej Antalík who will introduce the MiMiC framework for multiscale modeling in computational chemistry. "MiMiC enables flexible and efficient implementations of multiscale simulation methods with support for multiple subsystems through coupling external programs." Don't forget to register!

Ambassador of the month

We feature two members of our Ambassador Council: Hector Martinez-Seara, representing the Czech Republic, and Attilio Vargiu, representing Italy. Hector and Attilio tell us about themselves, their research interests and how they are working with BioExcel.

Publication: Combining HADDOCK and diffusion algorithms for antibody modelling

Recent work supported by BioExcel introduces a protocol to improve the modelling of challenging antibody H3 loops. Building upon the diffusion-based AlphaFlow algorithm, it is possible to obtain highly heterogeneous ensembles of conformations that can then be used in downstream modelling tasks, such as docking with HADDOCK. This work shows how accurate loop conformations and antibody-antigen complexes can be obtained even for extremely challenging antibody sequences. Learn more about it in the preprint by M Giulini, X Xu, and AMJJ Bonvin.

Publication: FAIR principles in biomolecular simulations

Some months ago we reported on our efforts together with the rest of the community to support the establishment of FAIR principles in biomolecular simulations. We are pleased to announce that our publication on "The need to implement FAIR principles in biomolecular simulations" is now a featured article on the Nature Methods homepage.

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!
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