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In this issue we provide updates on our main codes, including new version releases of GROMACS, HADDOCK and BioBB. We are open for registration and abstract submission for our 3rd BioExcel Conference on Advances in Biomolecular Simulations. Our webinar series continues to roll on throughout the next few months with a focus on GROMACS and talks by our Ambassadors featuring their software. You can read about our recent Ambassador workshop in Slovenia and our Ambassador of the month with two new Ambassadors featured, plus we highlight some examples of GROMACS/PMX being used for enzyme optimisation.
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The new version of GROMACS (2026.0) was released last month; check out the release notes. Join our webinar on 3rd March 2026 where Vedran Miletic, Lukas Müllender and Berk Hess will be going through the new features and performance improvements associated with this major release. Take a look at the section below on webinars for additional opportunities to learn about GROMACS.
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A new HADDOCK3 version (2025.11.0) was released at the end of last year where the use of restraints in the presence of ions in the flexref module was fixed (this bug was identified by a user) and support was added for non-standard ligand/molecules/residues in the alascan module.
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We have also added a workflow example for protein-zinc-finger docking: E2-E3 complex of UbcH5 and the zinc-finger domain of Not4 (docking with ions).
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A new BioBB version (2025.2) was released at the end of last year (notes here) and includes:
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- Major refactoring of the library's core to support folders as input and/or output parameters.
- All BioBB building blocks have been refactored to use a unified, Pythonic execution API, removing legacy CLI wrappers while preserving full functionality.
- BioBB library is now compatible with Python v3.10, v3.11 and v3.12 (BioBB Python Compatibility).
- All BioBB's have been updated to 5.2.0+ version.
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3rd BioExcel Conference on Advances in Biomolecular Simulations
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Registration and call for abstracts for the 3rd BioExcel Conference on Advances in Biomolecular Simulations opened on the 19th January.
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Our big event of 2026 will take place in Brno, Czech Republic from 27 to 30 September 2026 and we already have a great line-up of confirmed speakers. If you are interested in sponsoring the event we have a number of sponsorship packages available which will help you gain visibility and make the event more accessible to a greater number of students.
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BioExcel Webinar series: February-March 2026
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But, we are not stopping there!
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We have a number of additional webinars lined up for April and beyond so keep checking our website for further information.
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BioExcel software helps the development of environmentally friendly enzymes
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GROMACS and PMX running on the LUMI supercomputer are being used in the development of industrial enzymes solutions. Our codes are key in understanding enzyme-substrate interactions and during the optimisation of enzyme activity. Read more about it here.
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Publication highlighting the use of GROMACS / PMX for enzyme design
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Remaining on the topic of enzyme optimisation, we highlight a recent publication where the authors have developed a low computational cost workflow, incorporating GROMACS and PMX, that predicts changes in activation free energy barriers caused by mutations. You can read more about this work here.
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Ambassador Program workshop in Ljubljana, Slovenia
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Ambassadors of the month
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We feature Ezgi Karaca and Luca Monticelli, our Ambassadors representing Turkey and France respectively. They tells us about themselves, their research interests and how they are working with BioExcel.
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Request: please acknowledge BioExcel support
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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.
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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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