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In this edition of the BioExcel Newsletter we feature some important updates to all our software codes, including the release of a number of new and updated tutorials, and highlight some new publications on free energy calculations. We continue our 'Ambassador of the month' feature and highlight some job positions available through our Ambassador Program. Read our report on the recent Summer School on Biomolecular Simulations and mark your calendars for our key events coming in 2026!
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Wishing everyone a relaxing summer!
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BioExcel software development update
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The latest version of GROMACS (2025.2) was released last month. Check out the release notes which document the changes to fix known issues in version 2025.1. We are currently working on incorporating new features which will be part of the GROMACS 2026 release. You can follow GROMACS development via the GROMACS GitLab repo or by attending GROMACS developer calls which are held every second Wednesday at 11:00 or 17:00 CET.
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We have an updated version of the "Introduction to Molecular Dynamics" tutorial which now covers the use of multiple time-stepping and mass repartitioning algorithms to carry out 'faster simulations'. We also have a new "Density-fit simulation" tutorial which shows how to fit a protein to its cryo-EM density map.
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Haddock3, the new version of HADDOCK, has been officially released and is now available on GitHub. Redesigned with a modular architecture, Haddock3 allows users to create custom modelling/scoring/analysis/etc. workflows by combining selected modules. A corresponding paper has been published in J. Chem. Inf. Model. Further, Haddock3 is now available as a module on supercomputers LUMI (Finland) and DISCOVERER (Bulgaria).
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A number of new features have been added: Haddock3 now supports modification of the amino acid and nucleotide termini into charged or uncharged states. HADDOCK2.4 web-server and Haddock3 now support more modified amino acids: citrulline (CIR) and pyro-glutamic acid (PCA). Our utility haddock-restraints now can generate unambiguous restraints to hold small ligands in place during the docking.
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The new BioBB release (2025.1) is scheduled for July; incorporating Python v3.12 compatibility and major software dependencies updated to more recent versions: GROMACS v2024.5, Ambertools v22.5 and Haddock3 v2025.5.0. Also in July, the new BioBB Haddock3 demonstration workflow tutorial will be finalised, with the last rounds of testing currently being completed.
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Report: Summer School 2025 published
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The 8th edition of our Summer School on Biomolecular Simulations took place earlier this month in Sardinia. It's always a highlight for us and with a participant feedback score of higher than 9/10 we are confident that those attending enjoyed it as well. Read this year's report where we summarise the daily content and highlight the networking and community-building elements which are valued so much by attendees.
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Ambassador of the month
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We feature two members of our Ambassador Council: Anela Ivanova, representing Bulgaria, and Vlad Cojocaru, representing Romania. Anela and Vlad tell us about themselves, their research interests and how they are working with BioExcel.
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Publications: free energy calculations
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Upcoming BioExcel events in 2026
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2026 may still be some time away but we are already planning some major events: the Adriatic edition of our Ambassador Program workshop will take place 11-12 February, the 9th edition of our Summer School on Biomolecular Simulations will be in June and the 3rd edition of our BioExcel Conference on Advances in Biomolecular Simulations will be in October. Mark your calendars and keep an eye for updates on our website and digital media!
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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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