Issue 50 | August 2023
Dear reader,

Welcome back to our Newsletter following the summer break. We are pleased to announce our first workshop from the Ambassador Program which will take place in October. Earlier this month we released two new GROMACS tutorials and next week we will restart our webinar series with a presentation on a powerful computational chemistry workflow from AstraZeneca. We highlight two software publications connected to the new modular version of HADDOCK and some high-impact publications from some of our partners. Our collaboration with ELIXIR is developing a set of FAIR workflows to characterise and analyse native proteins. Finally, if you would like to know more about BioExcel be sure to watch our new BioExcel video which highlights the importance and value of the work we do. Check out the articles below for more information.

The BioExcel Team

BioExcel and EuroCC workshop

In collaboration with the National Competence Centres in Austria, Czechia, Slovakia and Hungary we are pleased to announce our first workshop from the Ambassador Program. The one and a half day workshop is open to all participants from EuroHPC Joint Undertaking members and will take place face-to-face from 18-19 October in Bratislava, Slovakia and online. The workshop will focus on GROMACS and HADDOCK and you can find further information and how to register by following the link to the event page on the BioExcel website.
Fast, flexible, Free, GROMACS

New GROMACS tutorials

We are pleased to announce the release of two new GROMACS tutorials. One tutorial will show you how to run a molecular dynamics simulation of a simple membrane protein step-by-step. The tutorial will go through both how to set up the input files, as well as how to set up all the steps from energy minimization to data production. The other tutorial will show you how to apply the accelerated weighted histogram (AWH) method to compute the free energy of solvation of a simple molecule. Both tutorials can be run online in a browser or downloaded to run on a local machine using an installed version of GROMACS.

Webinar: Maize workflows

We will restart our webinar series on 5 September with a presentation by Thomas Löhr from AstraZeneca who will talk about a powerful new workflow manager being developed at AstraZeneca to manage complex drug design pipelines. Find out more and register to hear this exciting presentation.

Software publications: new DeepRank version and ARCTIC-3D

We highlight two pre-print publications from Alexandre Bonvin's group at University of Utrecht, both of which have connections with HADDOCK3, the new BioExcel-funded modular version of HADDOCK. The new version of DeepRank greatly improves the performance and usability of the software and opens up new application opportunities, e.g. for antibody-antigen complexes. ARCTIC-3D is a fast and user-friendly data mining and clustering software to retrieve data and rationalise the interface information associated with protein input data.

BioExcel publication highlights

Our partners from Institute for Biomolecular Research (IRB) Barcelona and Nostrum are part of a publication in Nature Communications reporting the discovery of new non-canonical p38 alpha kinase inhibitors.
IRB has also contributed to a recent publication in the high impact journal Science on the discovery of splice variants of mitofusin 2, which tether mitochondria to the Endoplasmic Reticulum.
Of particular interest to those working on simulating DNA is a manuscript currently under review presenting a novel coarse-grained model of DNA capable of back-mapping the structure to all-atom resolution through a machine learning algorithm and thus, reproducing all-atom dynamics at a much lower computational cost.

Collaboration: FAIR workflows to characterise conformational states of proteins

"Characterizing the different conformational states of proteins and the transitions between them is critical for gaining insight into their biological function and can help explain the effects of genetic variants in health and disease and the action of drugs." BioExcel and the ELIXIR 3D-BioInfo structural community are collaborating to produce a set of FAIR workflows for the generation of conformational ensembles of native proteins and analysis of their flexibility.

New BioExcel video

The BioExcel Centre of Excellence has been running since 2015 and much has happened during that time, but we have always remained true to our mission: "Provide Life Sciences researchers with high-quality, user-friendly software. Increase their expertise and skills. Strengthen the community." In our new video you can find out more about why our work is critical for Life Science researchers to fully exploit the advances in available computing power and the impact it is having in key areas like drug discovery.

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!
twitter linkedin youtube