Issue 55 | June 2024
Dear reader,

We are happy to announce that our annual BioExcel Survey is now open. We are looking forward to getting your feedback to help us provide better software, support and services in future. Find out more about the most recent developments to our key software tools which have been influenced by the feedback provided by users through the individual software surveys we ran during 2023. The oral presentation deadline for the second BioExcel Conference on Advances in Biomolecular Simulations is in a couple of weeks so don't delay submitting your abstract. In this edition of the newsletter we provide some further information on two Ambassador Program events. We will return at the end of August with the next edition of the BioExcel Newsletter.

Wishing everyone a relaxing Summer!

The BioExcel Team

The BioExcel survey 2024 is open

From software development to training and support; don't miss out on your chance to influence what we do and how we do it! Your views are important to us so please complete our annual BioExcel survey. This year we have combined all our individual software surveys into one and added some more general questions about training, support and community engagement. The survey will remain open until the end of August and should only take about 15 minutes to complete.

BioExcel core software development updates

In this section we provide a short update on some of the recent work carried out on our core software applications. This work is based on the priorities which emerged from the 2023 user surveys and is reflected in our software development dashboard.


The beginning of May saw the minor release of GROMACS 2023.5 and the developers are now working hard to bring new features into the 2025 release. To follow GROMACS development you can look at GROMACS GitLab repo. If you are interested in coding in GROMACS, we will be running the second edition of the online workshop "Learn to code in GROMACS" from 10 to 12 September 2024. As always, you are welcome to post your questions on the user forum if you need help with your simulations. Keep yourself up to date by following GROMACS news at:


The HADDOCK team has been working hard to finalize the first production release of HADDOCK3 (still to come), solving many small issues and improving in particular the alanine scanning module and the presentation of results. In preparation for the 2024 BioExcel Summer School an updated HADDOCK3 tutorial has been published. In addition to demonstrating the use of HADDOCK3 for antibody-antigen modelling, this tutorial adds several "bonus" tasks, for example dissecting the interaction mode using our Arctic-3D server, comparison with with AlphaFold and, giving for the first time a glimpse into the new HADDOCK-webapp which is being developed in collaboration with the Netherlands e-Science Center. Together with the team of our BioExcel Ambassador Dr. Attilio Vargiu at the University of Cagliari we published a preprint on "Predicting binding events in very flexible, allosteric, multi-domain proteins", demonstrating the use of advanced enhanced sampling methods with GROMACS to generate bound-like conformations of very flexible and allosteric proteins bearing multiple binding sites, and then dock ligands into the resulting ensembles of conformations, comparing the performance of AutoDock and HADDOCK.


The PMX team is working on an updated release of the PMX web server along with a Conda packaging of the code. A novel absolute binding free energy tutorial is under preparation and should be published soon. We will also also publish some advancement on estimating errors originating from initial structure modelling in Relative Binding Free Energy calculations. If you have any questions related to PMX please post these in the user forum.

BioExcel Building Blocks (BioBB):

A new BioBB release (2024.1) is available which contains two new packages; a 'biobb_haddock' package (a module collection to compute information-driven flexible protein-protein docking) and a 'biobb_pytorch' package (a module collection to create and train ML & DL models using the popular PyTorch Python library). In addition, all BioBB workflows have new Docker images and Dockerfiles and are now available in Google Colab.
Scientific journals are starting to require reproducibility before publication and this is where BioBB can help. Check out the new publication on "Using interactive Jupyter Notebooks and BioConda for FAIR and reproducible biomolecular simulation workflows" and the recent BioExcel webinar on this topic.

Second BioExcel Conference: oral presentation deadline coming up

The early bird deadline has passed but we are still accepting abstract submissions for oral presentations until 15 July 2024. Make sure that you are part of this fantastic event! More information on registration and abstract submission.

Ambassador Program: November 2024 workshop in Coimbra, Portugal

As part of our Ambassador Program and in collaboration with our colleagues at the National Competence Centres for HPC in Portugal, France, Spain and Ireland we are organising a workshop from 26 to 28 November in Coimbra, Portugal. The workshop will cover the use of core BioExcel software codes and will include an Alphafold tutorial. For further information on the workshop check out our website.

Ambassador Program: April 2024 workshop in Riga, Latvia

As part of our Ambassador Program we organised a one-off workshop in collaboration with the Latvian Institute of Organic Synthesis in Riga entitled "Getting Started with BioBB and PMX: Open-Source Tools for Biophysical and Medicinal Chemistry Simulations". Contact us at if you are interested in hosting and co-organising this type of event in your own European country.

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 to let us know how we have helped you. Thank you for your continued support!
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