BioExcel provides expert support in the areas of biomolecular integrative modelling, molecular dynamics simulations, free energy calculations and docking. In response to the COVID-19 disease, BioExcel has launched a series of actions to support research on SARS-CoV-2. If you are working on modelling and simulations of systems related to SARS-CoV-2, please get in touch with us at firstname.lastname@example.org.
Ongoing partner efforts
Our partners are actively working on a range of modelling and simulation projects related to SARS-CoV-2. In addition, all partner supercomputing centers – PDC Center for High Performance Computing (Sweden), Barcelona Supercomputing Center (Spain), EPCC (UK) and Juelich Supercomputing Center (Germany) offer priority access to HPC infrastructure for the needs of COVID-19 research. Find out more on the BioExcel Center of Excellence in support of COVID-19 research page.
COVID-19 Molecular Structure and Therapeutics Hub
The Molecular Sciences Software Institute (MolSSI) and BioExcel consortium have set up a new COVID-19 Molecular Structure and Therapeutics Hub with COVID-19 biology and data. Join the data curation teams to review other groups’ submissions and submit your own data as well. Deposit any data including small molecules, models, simulation data and new targets to the contributing page. Please pass on your feedback to improve this resource to email@example.com.
A Community Letter Regarding Sharing Biomolecular Simulation Data for COVID-19
Sharing of data for COVID-19 applications has become vital more than ever due to the urgent need of lead identification for therapies, diagnostics, and vaccines for COVID-19. To maximize the impact of molecular simulation methods in this crisis, BioExcel members have signed the international community letter which aims to connect scientists and improve communication between simulation, experimental and clinical data investigators.
European digital infrastructures in support of coronavirus research
Several European research communities and infrastructures are currently joining forces through highly complementary activities to help researchers in addressing the current outbreak and finding a treatment for the novel coronavirus. Many e-Infrastructures such as HADDOCK are trying to make the most of the available data. Read more here.
HADDOCK to support COVID-19 research
In the context of COVID-19 related research, the WeNMR portal has seen an increase of registrations over the last weeks with many users indicating they intend to use it for COVID-19 projects.
Simulation of the viral SARS-CoV-2 spike protein
In a collaborative effort , the MPG, UU, JYU and KTH teams simulate the viral SARS-CoV-2 spike protein receptor binding domain (left) complexed with the human ACE2 receptor (right). Using a combination of the GROMACS and PMX software, several interface residues (highlighted in blue) have been identified on the receptor that, when mutated, lead to a higher predicted affinity and therefore may guide vaccine development.
Launch of BioExcel-CV19 web-server interface
The online platform BioExcel-CV19 has been launched to provide web-access to atomistic-MD trajectories for macromolecules involved in the COVID-19 disease The project is part of the open access initiatives promoted by the world-wide scientific community to share information about COVID-19 research.
IMI announces COVID projects, boosts funding pot to EUR 72 million
The Innovative Medicines Initiative has provisionally selected 8 projects for funding from its fast-track Call for proposals on coronavirus diagnostics and treatments. Among the projects, Corona accelerated R&D (CARE) in Europe has received funding to deliver treatments for the current COVID outbreak as well as future coronavirus outbreaks, with Utrecht University as key partner.
Launch of Workflow Hub
The Workflow Hub was accelerated by COVID to find cheminformatics workflows such as the virtual screening of the SARS-CoV-2 main protease. With an early focus for COVID workflows and now a broadened functionality, it is listed in the COVID-19 Data Portal as a related resource. BioExcel is a contributing partner to the Workflow Hub.
Provenance and metadata standards for COVID-19 data
A community standard for packaging data with rich metadata, Research Object Crate (RO-Crate) was initiated by BioExcel and has grown in. In collaboration with the BY-COVID project we have developed specializations of RO-Crate to capture provenance of computational workflows, which will be used in conjunction with automated registrations in the EU-wide COVID-19 Data Portal.
Endorsement of Manifesto for EU COVID-19 Research
BioExcel is proud to endorse the manifesto for EU-COVID-19 Research. In July, the Commission launched the Manifesto for EU Covid-19 Research, as part of the European response to the coronavirus outbreak and since it’s launch celebrates 2000 signatories.