Issue 47 | February 2023
Dear reader,

Read about the kick-off meeting we held in Stockholm and some of our plans for phase 3 of BioExcel. Also this month, we have released a new version of GROMACS and are aiming to start our webinar series talking about what is new in GROMACS 2023, so keep an eye out for this! Our ongoing collaboration with AstraZeneca has delivered an open-source workflow which incorporates PMX and GROMACS to facilitate the calculation of protein-ligand relative binding free energies. Check out the news below for more information.

The BioExcel Team
From L to R: Javier Iglesias (NBD), Adam Hospital (IRB), Rodrigo Honorato (UU), Pau Andrio (BSC), Berk Hess (KTH), Erwin Laure (MPG), Richard Norman (NC), Alessandra Villa (KTH), Tiina Leiponen (CSC), Atte Silanpää (CSC), Alexandre Bonvin (UU), Erik Lindahl (KTH), Rossen Apostolov (KTH), Farzaneh Jalalypour (KTH)

BioExcel-3 kick-off meeting

This month we held our BioExcel-3 kick-off meeting in Stockholm. It was a great opportunity to discuss our plans for phase three and see some old and some new faces, as we welcomed CSC to the team.
Our work will focus on improving the performance of our world-leading biomolecular software and ease its usability through a range of scientific workflows and associated deployment environments. We will be stepping up our efforts to gather and implement user needs and are currently devising a way to do this more efficiently. Support for the community remains at the center of what we do and through our dissemination and training activities our focus will be on growing and strengthening the community, broadening our outreach and achieving greater impact. Our brand new Ambassador Program focused on engaging with EU13 countries will help us achieve this.
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GROMACS 2023 version released

The code, manual, release notes, installation instructions and test suite can be found on the GROMACS website where you can also check out the highlights. If you have any questions or require support go to the GROMACS section of Ask BioExcel.

PMX/GROMACS workflow for automated relative binding free energy calculations

Our development of an open-source automated workflow for end-to-end generation of ligand binding free energies from SMILES strings is an important step to lowering the access barrier to performing these calculations routinely during computational drug discovery endeavours.
Our flexible workflow "provides a scalable, flexible and reproducible method of executing free energy calculations and allows for straightforward distribution, parallelisation and monitoring of calculations using either local or cloud computing resources. The modular nature of the workflow enables substitution of the blocks allowing to easily combine open source and commercial software packages."
The work describing the development and implementation of the workflow can be accessed through the preprint publication and the Icolos workflow manager code-base is available through a GitHub repository.
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