{"id":91293,"date":"2024-01-09T16:12:57","date_gmt":"2024-01-09T15:12:57","guid":{"rendered":"https:\/\/www.pcb.ub.edu\/bioexcel-cv19-a-breakthrough-in-understanding-sars-cov-2-proteins\/"},"modified":"2024-01-09T18:18:25","modified_gmt":"2024-01-09T17:18:25","slug":"bioexcel-cv19-a-breakthrough-in-understanding-sars-cov-2-proteins","status":"publish","type":"post","link":"https:\/\/www.pcb.ub.edu\/en\/bioexcel-cv19-a-breakthrough-in-understanding-sars-cov-2-proteins\/","title":{"rendered":"BioExcel-CV19: a breakthrough in understanding SARS-CoV-2 proteins"},"content":{"rendered":"

Researchers at IRB Barcelona<\/a>‘s Molecular Modelling and Bioinformatics lab publish in the journal<\/strong> Nucleic Acids Research\u00a0a revolutionary database for molecular dynamics simulations: BioExcel-CV19<\/a>. 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.<\/strong><\/p>\n

Designed to meet the urgent need for insights into the molecular intricacies of SARS-CoV-2 infection, BioExcel-CV19<\/a>\u00a0is a repository for Molecular Dynamics (MD) simulations. Researchers at IRB Barcelona, led by\u00a0Dr. Modesto Orozco<\/strong>, 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.<\/p>\n

\u201cThis database represents a shift in molecular dynamics databases, built to handle large systems and long trajectories while seamlessly integrating with modern MD simulations\u201d, explains\u00a0Orozco<\/strong>, head of the Molecular Modelling and Bioinformatics<\/a> lab at IRB Barcelona and University of Barcelona professor. \u201cIt brings together trajectories contributed by diverse research groups, showcasing a collaborative approach that drives scientific discoveries,\u201d he adds.<\/p>\n

The article, published in\u00a0Nucleic Acids Research, not only highlights the features of\u00a0BioExcel-CV19but also underscores the importance of storing MD simulations. Stored simulations ensure result reproducibility and facilitate community-wide analysis. \u201cPlatforms like BioExcel-CV19 should become a standard, akin to the Protein Data Bank (PDB) in structural biology,\u201d states\u00a0Dr. Adam Hospital<\/strong>, a Research Associate at IRB Barcelona, who has led this work together with Dr. Orozco<\/strong>.<\/p>\n

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.<\/p>\n

In the field of biomolecular simulation,\u00a0BioExcel-CV19\u00a0provides 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.<\/p>\n

\u00bb Reference article:<\/strong>\u00a0Daniel Beltr\u00e1n, Adam Hospital, Josep Llu\u00eds Gelp\u00ed, Modesto Orozco, A new paradigm for molecular dynamics databases: the COVID-19 database, the legacy of a titanic community effort,\u00a0Nucleic Acids Research<\/em>, Volume 52, Issue D1, 5 January 2024, Pages D393\u2013D403, \u00a0DOI:\u00a010.1093\/nar\/gkad991<\/a><\/p>\n

\u00bb Related news:<\/strong> IRB Barcelona website [+]<\/a><\/p>\n","protected":false},"excerpt":{"rendered":"

Researchers at IRB Barcelona‘s Molecular Modelling and Bioinformatics lab publish in the journal Nucleic Acids Research\u00a0a revolutionary database for molecular dynamics simulations: BioExcel-CV19. 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