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Laying the groundwork for future molecular dynamics databases

A new database of molecular dynamics simulations helps further scientific insight into COVID-19 proteins.

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Researchers from Barcelona, Spain, have developed a free and open repository for molecular dynamics (MD) simulations called BioExcel-CV19. Supported by the EU-funded MDDB and BioExcel-2 and BioExcel-3 projects, the database will help shed light on the molecular intricacies of SARS-CoV-2 infection. Its features are described in a paper published in ‘Nucleic Acids Research’. A huge volume of data is generated worldwide from MD simulations that analyse the physical movements of atoms and molecules. However, this data is usually not open to the scientific community. Also, up to now, efforts to make MD data safe and reusable have been based on simple databases that fail to offer current MD users a true solution because they only provide a limited set of standard analyses on single-short trajectories. What scientists need is a database that enables flexible analyses and has the ability to handle large systems. Enter BioExcel-CV19.

A shift in MD databases

The platform gives scientists web access to atomistic MD trajectories of macromolecules implicated in COVID-19. Important information included offers insight into the roles of key SARS-CoV-2 proteins, including the spike protein, angiotensin converting enzyme 2, receptor binding domain, polymerase, nucleoproteins and membrane proteins. As of August 2023, the database contains over 10 000 trajectories. The resulting trajectories are presented along with a set of quality control analyses and system information. All data produced by the project is available to download from a REST application programming interface. An app called Jupyter Notebooks has also been integrated into the platform, allowing fully customised meta-analysis by final users. There are no login requirements for BioExcel-CV19, which is free and open to all users. “This database represents a shift in molecular dynamics databases, built to handle large systems and long trajectories while seamlessly integrating with modern MD simulations,” remarks study senior author Dr Modesto Orozco of MDDB project coordinator and BioExcel-2 and BioExcel-3 project partner Institute for Research in Biomedicine (IRB Barcelona), Spain, in a ‘EurekAlert!’ news release. “It brings together trajectories contributed by diverse research groups, showcasing a collaborative approach that drives scientific discoveries,” the researcher adds. The database will have an impact on scientific domains such as virology, genomics, structural and molecular biology, drug design, machine learning and biomolecular simulation. Where biomolecular simulation is concerned, scientists can use the large amounts of data available on BioExcel-CV19 to refine algorithms and MD force fields. Reanalysing and reusing data creates opportunities for new meta-analyses and discoveries. “Platforms like BioExcel-CV19 should become a standard, akin to the Protein Data Bank (PDB) in structural biology,” states study co-author Dr Adam Hospital, also of IRB Barcelona, who has led this work together with Dr Orozco. The BioExcel-2 (BioExcel Centre of Excellence for Computational Biomolecular Research) project ended in 2022. MDDB (Molecular Dynamics Data Bank. The European Repository for Biosimulation Data) and BioExcel-3 (BioExcel Centre of Excellence for Computational Biomolecular Research) end in 2026. For more information, please see: MDDB project BioExcel project website

Keywords

MDDB, BioExcel-2, BioExcel-3, COVID-19, SARS-CoV-2, molecular dynamics, protein, data, database, biomolecular

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