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Top-view domain representation of the SARS-CoV-2 Spike protein, available in the new BioExcel-CV19 Molecular Dynamics Database. Image / IRB Barcelona.

BioExcel-CV19: a breakthrough in understanding SARS-CoV-2 proteins

Researchers at IRB Barcelona‘s Molecular Modelling and Bioinformatics lab publish in the journal Nucleic Acids Research a revolutionary database for molecular dynamics simulations: BioExcel-CV19. Future team efforts will focus on advancing the platform, ensuring it evolves with the ever-changing landscape of COVID-19 research, as well as continually updating it with new simulations and user-suggested analyses, fostering ongoing collaborations and discoveries.

Designed to meet the urgent need for insights into the molecular intricacies of SARS-CoV-2 infection, BioExcel-CV19 is a repository for Molecular Dynamics (MD) simulations. Researchers at IRB Barcelona, led by Dr. Modesto Orozco, have built this database including key flexibility information essential for understanding the roles of key proteins in the virus, such as the Spike protein, Receptor Binding Domain (RBD), and RNA-dependent RNA polymerase (RdRp), providing over 10,000 trajectories.

“This database represents a shift in molecular dynamics databases, built to handle large systems and long trajectories while seamlessly integrating with modern MD simulations”, explains Orozco, head of the Molecular Modelling and Bioinformatics lab at IRB Barcelona and University of Barcelona professor. “It brings together trajectories contributed by diverse research groups, showcasing a collaborative approach that drives scientific discoveries,” he adds.

The article, published in Nucleic Acids Research, not only highlights the features of BioExcel-CV19but also underscores the importance of storing MD simulations. Stored simulations ensure result reproducibility and facilitate community-wide analysis. “Platforms like BioExcel-CV19 should become a standard, akin to the Protein Data Bank (PDB) in structural biology,” states Dr. Adam Hospital, a Research Associate at IRB Barcelona, who has led this work together with Dr. Orozco.

BioExcel-CV19’s impact extends to various scientific domains, including virology, genomics, structural and molecular biology, drug design, biomolecular simulation, and machine/deep learning. The open data provided becomes a valuable resource for training models, influencing fields that use data for various purposes.

In the field of biomolecular simulation, BioExcel-CV19 provides a wealth of data for refining algorithms and MD force fields. The potential for re-analysis and reuse of data opens avenues for new discoveries and meta-analyses, making BioExcel-CV19 a valuable asset for the scientific community.

» Reference article: Daniel Beltrán, Adam Hospital, Josep Lluís Gelpí, Modesto Orozco, A new paradigm for molecular dynamics databases: the COVID-19 database, the legacy of a titanic community effort, Nucleic Acids Research, Volume 52, Issue D1, 5 January 2024, Pages D393–D403,  DOI: 10.1093/nar/gkad991

» Related news: IRB Barcelona website [+]