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This issue of the newsletter is packed full of news following the summer break. As well as updates on our main codes we highlight the work we have been doing on our showcases. These showcases take our codes to a new level of applicability, scalability and usability! This year's BioExcel survey is now officially open and we ask you to kindly take a few minutes to provide your views. We have a new special edition webinar coming in September as well as highlights regarding new collaborations, publications and tutorials. Read on for all this and more!
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BioExcel software development update
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The GROMACS development team is currently working on the new release (2026) which will be coming out early next year.
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A number of new features have been added to HADDOCK2.5 in the 2025 official hot-summer-release, and this is now the version running behind the HADDOCK web portal.
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Added support for pyroglutamic acid (PCA)
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Modified analysis to write stage-specific CNS average job files
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Simplified CNS execution scripts
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Added check of coordinates for consistency with the PDB format
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For HADDOCK3, each code update will be reflected in the haddock version. The current version (v2025.8.0) corresponds to this year (2025), month 8 (August), and zero after '8' indicates that, for now, no code updates took place in August. v2025.8.0comes with some new features compared to v2025.5.0:
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Alascan module has been optimised to make better use of parallel tasks - now calculations are parallelized per-residue rather than per-model
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Added the computation of standard deviation in alascan module and plotting error bars
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Added the values of covalent bond energy in the PDB header out of generated models
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Added two new supported non-canonical residues, pyroglutamic acid (PCA) and Citruline (CIR)
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Added guardrail for the [rigidbody] module, i.e. a check that either any kind of restraints file(s) are supplied, or that one of the viable for ab-inito docking parameters are enabled, e.g. centre of mass restraints.
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The haddock-restraints v0.9.0 software allows generating various types of restraints to guide HADDOCK simulations. You can access the user guide and webserver (work in progress) for these.
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The new BioBB version (2025.1) has been released with several updates; check out the release notes.
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HPC workflows (GitHub) have been updated to the new release and benchmarks run at BSC Marenostrum 5 supercomputer using the Free Energy Calculation workflows (including GROMACS, PMX and PyCOMPSs).
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We are also currently working on finalizing the BioBB Protein-Membrane MD analysis tutorial demonstration workflow (GitHub).
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Showcases: new capabilities, improved scalability and enhanced usability of the BioExcel codes
We highlight our five current showcases which illustrate the increased applicability of the GROMACS, HADDOCK and BioBB software and workflows. These showcases are driven by a user-centric approach, ensuring that both academic and industrial needs shape the evolution of the different software:
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BioExcel survey 2025 & your feedback
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Feedback from our community and our users is very important to us. We have officially opened our BioExcel Survey 2025 where you can help influence the development of our main codes and more.
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In addition, we have a new area for 'your feedback' which will be available for as long as BioExcel is running for you to share your thoughts on anything to do with BioExcel.
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We really appreciate you taking the time to complete the survey and share your views!
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Special Edition Webinar: Summer School 2025 poster prize winners
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Publications and new tutorial for nanobody-antigen modelling using HADDOCK3
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A preprint describing the use of HADDOCK3 for the modelling of nanobody-antigen complexes has been published: Miguel Sánchez-Marín, Marco Giulini, Alexandre M.J.J. Bonvin. "Combining AI structure prediction and integrative modelling for nanobody-antigen complexes." bioRxiv 2025.07.01.662355; DOI:10.1101/2025.07.01.662355. A corresponding nanobody-antigen modelling tutorial for HADDOCK3 is also available. Related to this, our work on improving the modelling of antibody-antigen complexes from clustered generative modelling ensembles which we highlighted in our April 2025 newsletter (#60) is now published in Bioinformatics Advances. DOI:10.1093/bioadv/vbaf161
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Collaboration: building commercialisation capabilities
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European Centres of Excellence can have a lasting impact beyond their research objectives by expanding their scope to offer services which solve concrete industry challenges. BioExcel together with the Centres of Excellence EXCELLERAT, ESiWACE3, HiDALGO2, ChEESE, MultiXscale and the CASTIEL project, are proud to present a new white paper designed to support the long-term sustainability of CoEs in HPC.
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EGI interview with Prof. Alexandre Bonvin: empowering Structural Biology
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Read the recent interview published in the EGI magazine with our very own Prof. Alexandre M.J.J. Bonvin where he talks about WeNMR, a worldwide infrastructure for NMR and Structural Biology, the HADDOCK software, which is now serving over 66,000 users in 174 countries (almost 90% of all existing countries!), and more!
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-- HADDOCK’s success is built on a user-friendly web server, strong support and training, and a commitment to scientific excellence --
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Upcoming BioExcel events in 2026
As announced in the previous edition of our newsletter, we have some major events coming up in 2026 with dates now confirmed:
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- The Adriatic edition of our Ambassador Program workshop will take place 11-12 February in Ljubljana, Slovenia.
- The 9th edition of our Summer School on Biomolecular Simulations will be held 7-12 June in Sardinia, Italy.
- The 3rd edition of our BioExcel Conference on Advances in Biomolecular Simulations will be held 27-30 September in Brno, Czech Republic.
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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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