In this issue we provide updates on our main codes, including two GROMACS patch releases and a major refactoring of the BioBB code. If free energy calculations are of interest to you check out the charge model evaluation study which we just published. Further information on our workshop in Slovenia in February is now available and registration opens next week. Also, our annual survey closes today so this is your last chance to provide us with feedback.
Last month saw two patch releases for the GROMACS versions which are currently under active maintenance. Click on each to access the release notes; GROMACS 2025.3 and GROMACS 2024.6. In early December we will be hosting a GROMACS webinar where we will cover some of the latest features and functionality. Keep an eye out for this on our website and digital media channels.
HADDOCK3 2025.9.0 ships with the haddock-restraints software that allows easy creation of various types of restraints for HADDOCK, contains a new notebooks directory (see tutorials below) and has added support for THR-glycosylation.
HADDOCK2.5 and HADDOCK3 (release 2025.8.0) are now part of the SBGrid software offering.
A major refactoring of the BioBB library's code has taken place to support folders as input and/or output parameters within building blocks. Previously, only individual files were permitted. This enhancement unlocks new possibilities for workflows that depend heavily on folder-based data structures, such as enhanced sampling methods.
The first workflow to benefit from this upgrade has been the HADDOCK BioBB workflow. In its latest version, it runs more efficiently by eliminating the need to zip and unzip folders between steps. Instead, the folder is passed directly as a parameter, streamlining data handling and improving overall performance.
Integration of enhanced sampling methods such as Replica Exchange and Accelerated Weight Histogram (AWH) are currently in development.
If you haven't provided us with you feedback this is a great opportunity to do so and to influence the development of our main codes.
Publication: Charge Model evaluation in Free-Energy Calculations
Hot off the press! Accurate binding free energy prediction is key for efficient drug discovery. In this study we assess the performance of the GAFF2/ABCG2 parametrization in protein-ligand relative binding free-energy simulations using non-equilibrium alchemy. Read the publication by Behera, Gapsys & de Groot (2025) to learn more.
Ambassador Program workshop: February 2026 in Ljubljana, Slovenia
Next week (5th November) we will be opening the registration for the Adriatic edition of our Ambassador Program workshop which will take place 11-12 February 2026in Ljubljana, Slovenia.
The workshop is organised in collaboration with our colleagues at the National Competence Centres for HPC in Slovenia, Croatia and Italy and will cover the use of some of the core BioExcel software codes.
Ambassador of the month
We feature David de Sancho, our Ambassador representing Spain. David tells us about himself, his research interests and how he is working with BioExcel.
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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