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In this issue we provide updates on our main codes, including new releases for HADDOCK and BioBB. We have finalised the lineup of invited speakers for what should be an excellent BioExcel Conference on Advances in Biomolecular Simulations - don't forget to register and submit your abstract for the event. Our yearly survey (shorter than usual) is now open so please provide your feedback and help guide the future development of BioExcel. Our webinar series continues into May before we take a pause during the summer, after which we have two new Ambassador workshops scheduled for late summer and early autumn. Read on for all this and more!
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- Fixed incorrect handling of hetero atoms during CAPRI evaluation, ensuring accurate scoring.
- Corrected preprocessing when splitting structures containing MODEL records to avoid malformed inputs.
- Added the correct type handling for the seed option in the random_removal command to prevent runtime errors.
- Restored missing NGA glycan parameters, resolving issues with glycan-containing systems.
- Added a missing example to resolve a reported workflow issue affecting several refinement modules.
- Added automated topology/parameter generation for unknown small molecules, simplifying preparation of new ligands.
- Implemented interface-ligand RMSD–based clustering for protein–ligand examples, improving analysis of docking results.
- Added a runtime fallback to the local scheduler when GRID resources are unavailable, improving execution robustness.
Examples and Documentation:
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- Added new examples demonstrating workflows and resolving previously reported usage issues.
- Expanded example coverage for protein–ligand clustering workflows.
A new HADDOCK2.5 March 2026 release (fresh spring edition):
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- Added missing improper parameters for NGA glycan
- Corrected bug causing automatic reduction of the cluster size for reclustering to fail
- Added support for THR glycosylation
Benchmarks, new tutorials, new workflows, code usage in research:
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- BioBB modules used in all the workflows updated to the last version
- Refactoring of the workflows notebooks to make them compatible with Google Colab (after the incompatibilities found with condacolab library used in previous releases)
- New workflow "flavour": Apache AirFlow, using CWL specifications
- The new versions are all available from WorkflowHub, with independent DOIs to cite them.
- Three brand new demonstration workflows:
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Invited speaker line-up finalised!
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We have a truly outstanding line-up of invited speakers for our 3rd BioExcel Conference on Advances in Biomolecular Simulations taking place in Brno, Czech Republic from 27 to 30 September 2026.
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Our two keynote speakers; Richard BONNEAU (Roche and Genentech) and Helmut GRUBMÜLLER (Max Planck Institute) will be joined by Marc BAADEN (CNRS), Philip BIGGIN (University of Oxford), Alexandre BONVIN (University of Utrecht), Zoe COURNIA (Academy of Athens), Roberto COVINO (Goethe University Frankfurt), Vytautas GAPSYS (Johnson & Johnson Innovative Medicine), Gerrit GROENHOF (University of Jyväskylä), Ville KAILA (University of Stockholm), Ezgi KARACA (Dokuz Eylul University), Modesto OROZCO (Institute for Research in Biomedicine), Silvia OSUNA (Universitat de Girona) and Ilpo VATTULAINEN (University of Helsinki)
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Join them as a selected speaker by submitting your oral presentation abstract by 31st May 2026 (deadline extended). Full instructions on registration and abstract submission can be found on the conference webpage. Also note that the early bird registration deadline is 31st May 2026.
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BioExcel survey 2026
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Feedback from our users and community members is very important to us.
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The BioExcel survey 2026 gives you the opportunity to help guide our software development, support and training. This year the survey is shorter and we have included some questions on the impact of AI on biomolecular simulations and a dedicated (optional) section for industry users.
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We really appreciate you taking the time to complete the survey and share your views before the 30th of June!
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Webinars May 2026
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We have two excellent webinars coming up in May by two of our BioExcel Ambassadors;
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Ambassador Program workshops: Baltic and Aegean editions
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The dates are set for our 5th and 6th Ambassador Program workshops happening in Poland and Greece respectively later in 2026.
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The Baltic edition workshop will take place in Gliwice, Poland from 8 to 9 of September and will focus on the use of GROMACS, PMX and BioBB. Registration opens soon!
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The Aegean edition workshop will take place in Athens, Greece from 18 to 20 November and will focus on the use of GROMACS, HADDOCK and BioBB. Save the dates!
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BioExcel Ambassador of the month
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We feature Zoe Cournia, our Ambassador representing Greece. She tells us about herself, her research interests and how she is working with BioExcel.
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2026 Spring School in Computational Chemistry materials available
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Learning materials used during the recent 2026 Spring School in Computational Chemistry are available online!
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This year, in response to participant feedback, the school focused fully on simulation methods. The traditional 'AI in chemistry' part will be covered by a separate event scheduled for autumn 2026 and co-organised with the LUMI AI Factory.
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Beyond lectures and hands-on exercises, the school offers a poster session, ample time for discussion and a taste of Finnish culture. Registration for the 2027 edition will open towards the end of this year.
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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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