ArticleNucleic acids research2024
A new paradigm for molecular dynamics databases: the COVID-19 database, the legacy of a titanic community effort.
Article in Nucleic acids research, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed, 34 citations in OpenAlex.
- hexABC seeking the physical code of DNA.Nature communications · 2026Article
- MDCompress: better, faster compression of molecular dynamics simulation trajectories.Bioinformatics (Oxford, England) · 2026Article
- DynaRepo: the repository of macromolecular conformational dynamics.Nucleic acids research · 2026Article
- Atomistic Polymer Modeling: Recent Advances and Challenges in Building and Parametrization Workflows.Macromolecules · 2025Review
- mdBIRCH for Fast, Scalable, Online Clustering of Molecular Dynamics Trajectories.bioRxiv : the preprint server for biology · 2025Article
- Gromacs MetaDump: a tool for extracting GROMACS simulation metadata.Journal of cheminformatics · 2025Article
- PEGASUS: Prediction of MD-derived protein flexibility from sequence.Protein science : a publication of the Protein Society · 2025Article
- Beyond static structures: protein dynamic conformations modeling in the post-AlphaFold era.Briefings in bioinformatics · 2025Review
- Nearl: extracting dynamic features from molecular dynamics trajectories for machine learning tasks.Bioinformatics (Oxford, England) · 2025Article
- Robustness in biomolecular simulations: Addressing challenges in data generation, analysis, and curation.Cell reports. Physical science · 2025Article
- A Reflection on the Use of Molecular Simulation to Respond to SARS-CoV-2 Pandemic Threats.The journal of physical chemistry letters · 2025Review
- The need to implement FAIR principles in biomolecular simulations.Nature methods · 2025Article
- A FAIR-Compliant Management Solution for Molecular Simulation Trajectories.Journal of chemical information and modeling · 2025Article
- Article
- mdCATH: A Large-Scale MD Dataset for Data-Driven Computational Biophysics.Scientific data · 2024Article
- Adsorption-Driven Deformation and Footprints of the RBD Proteins in SARS-CoV-2 Variants on Biological and Inanimate Surfaces.Journal of chemical information and modeling · 2024Article
- Developments and applications of the OPTIMADE API for materials discovery, design, and data exchange.Digital discovery · 2024Article
- Bioinformatics and molecular biology tools for diagnosis, prevention, treatment and prognosis of COVID-19.Heliyon · 2024Review
- Pathways to a Shiny Future: Building the Foundation for Computational Physical Chemistry and Biophysics in 2050.ACS physical chemistry Au · 2024Review
- The 2024 Nucleic Acids Research database issue and the online molecular biology database collection.Nucleic acids research · 2024Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
Abstract
Molecular dynamics (MD) simulations are keeping computers busy around the world, generating a huge amount of data that is typically not open to the scientific community. Pioneering efforts to ensure the safety and reusability of MD data have been based on the use of simple databases providing a limited set of standard analyses on single-short trajectories. Despite their value, these databases do not offer a true solution for the current community of MD users, who want a flexible analysis pipeline and the possibility to address huge non-Markovian ensembles of large systems. Here we present a new paradigm for MD databases, resilient to large systems and long trajectories, and designed to be compatible with modern MD simulations. The data are offered to the community through a web-based graphical user interface (GUI), implemented with state-of-the-art technology, which incorporates system-specific analysis designed by the trajectory providers. A REST API and associated Jupyter Notebooks are integrated into the platform, allowing fully customized meta-analysis by final users. The new technology is illustrated using a collection of trajectories obtained by the community in the context of the effort to fight the COVID-19 pandemic. The server is accessible at https://bioexcel-cv19.bsc.es/#/. It is free and open to all users and there are no login requirements. It is also integrated into the simulations section of the BioExcel-MolSSI COVID-19 Molecular Structure and Therapeutics Hub: https://covid.molssi.org/simulations/ and is part of the MDDB effort (https://mddbr.eu).
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.