By Adam Hospital and Richard Norman
Collaborations with external institutions and close engagements with relevant national and international initiatives are important to promote our technology developments, share expertise and ensure that our work has significant scientific and societal impact.
BioExcel has established a collaboration with the EU-funded Human Brain Project (HBP) through our partners, IRB Barcelona and the Barcelona Supercomputing Center (BSC). The HBP is a long-term digital research initiative focused on understanding the complex structure and function of the human brain and how this can lead to the discovery of pharmaceutical agents for diseases affecting the brain and the rest of the Central Nervous System (CNS).
During the session on atomistic and Molecular Dynamics (MD) in the brain at the recent Euro Nano Forum 2023 event in Sweden, Adam Hospital (IRB Barcelona) talked about exploring the dynamics of CNS molecules in the context of the EBRAINS infrastructure, an open research digital ecosystem for neuroscience research. BioExcel’s contribution to this ecosystem is particularly evident under the ‘Molecular Tools’ collaboratory section. Here, researchers can access the BioExcel-Covid19 platform, a database providing access to atomistic-MD trajectories for macromolecules involved in COVID-19 disease, and the BioExcel Building Blocks (BioBB) software library which facilitates the setup and execution of complex biomolecular workflows.
The BioExcel-Covid19 platform was set up in early 2020 as part of the response by the world-wide scientific community to the SARS-CoV-2 outbreak. The database and associated webserver facilitate access to over 450 MD trajectories and associated analyses of Covid-19 related proteins such as the virus spike protein and human Angiotensin-converting enzyme 2 (hACE2). Scientists interested in Covid-19 research can explore the structural features resulting from the simulations in an interactive way.
The BioBB software library is a collection of Python wrappers on top of popular biomolecular simulation tools such as the GROMACS MD engine. BioBB provide a level of interoperability between the different computational tools and enable reproducibility of simulation results. Demonstration workflows using Jupyter Notebooks are available for setting up and running protein-ligand docking, MD simulations and free energy calculations. BioBB coupled with the associated database of CNS drug-like ligands available in EBRAINS, provide a toolset which can speed up in silico drug discovery.
The above were all featured in a recent training event on tools for Molecular Simulation of Neuronal Signaling Cascades held in Germany.
As part of BioExcel’s commitment to raise awareness of our software and services and provide training to increase the competence of our users we will be organising further events in the future. Please follow us on Twitter and LinkedIn (see bottom of this page) to gain visibility of these.