ArticleNucleic acids research2016
BIGNASim: a NoSQL database structure and analysis portal for nucleic acids simulation data.
Article in Nucleic acids research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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33 citing papers in PubMed, 82 citations in OpenAlex.
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- 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
- Systematic study of hybrid triplex topology and stability suggests a general triplex-mediated regulatory mechanism.Nucleic acids research · 2025Article
- Developments and applications of the OPTIMADE API for materials discovery, design, and data exchange.Digital discovery · 2024Article
- Pathways to a Shiny Future: Building the Foundation for Computational Physical Chemistry and Biophysics in 2050.ACS physical chemistry Au · 2024Review
- CGeNArate: a sequence-dependent coarse-grained model of DNA for accurate atomistic MD simulations of kb-long duplexes.Nucleic acids research · 2024Article
- A new paradigm for molecular dynamics databases: the COVID-19 database, the legacy of a titanic community effort.Nucleic acids research · 2024Article
- From complex data to clear insights: visualizing molecular dynamics trajectories.Frontiers in bioinformatics · 2024Review
- Perspectives on Ligand/Protein Binding Kinetics Simulations: Force Fields, Machine Learning, Sampling, and User-Friendliness.Journal of chemical theory and computation · 2023Review
- Structural analysis of the Candida albicans mitochondrial DNA maintenance factor Gcf1p reveals a dynamic DNA-bridging mechanism.Nucleic acids research · 2023Article
- Controlled sulfur-based engineering confers mouldability to phosphorothioate antisense oligonucleotides.Nucleic acids research · 2023Article
- Correlated motions in DNA: beyond base-pair step models of DNA flexibility.Nucleic acids research · 2023Article
- DNA double-strand break-derived RNA drives TIRR/53BP1 complex dissociation.Cell reports · 2022Article
- Applications of Molecular Dynamics Simulation in Protein Study.Membranes · 2022Review
- Development of Force Field Parameters for the Simulation of Single- and Double-Stranded DNA Molecules and DNA-Protein Complexes.The journal of physical chemistry. B · 2022Article
- Pre-exascale HPC approaches for molecular dynamics simulations. Covid-19 research: A use case.Wiley interdisciplinary reviews. Computational molecular science · 2022Article
- The Impact of the HydroxyMethylCytosine epigenetic signature on DNA structure and function.PLoS computational biology · 2021Article
- Sequence-specific dynamics of DNA response elements and their flanking sites regulate the recognition by AP-1 transcription factors.Nucleic acids research · 2021Article
- Using Open Data to Rapidly Benchmark Biomolecular Simulations: Phospholipid Conformational Dynamics.Journal of chemical information and modeling · 2021Article
Corrections and comments
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Authors and funding
11 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Molecular dynamics simulation (MD) is, just behind genomics, the bioinformatics tool that generates the largest amounts of data, and that is using the largest amount of CPU time in supercomputing centres. MD trajectories are obtained after months of calculations, analysed in situ, and in practice forgotten. Several projects to generate stable trajectory databases have been developed for proteins, but no equivalence exists in the nucleic acids world. We present here a novel database system to store MD trajectories and analyses of nucleic acids. The initial data set available consists mainly of the benchmark of the new molecular dynamics force-field, parmBSC1. It contains 156 simulations, with over 120 μs of total simulation time. A deposition protocol is available to accept the submission of new trajectory data. The database is based on the combination of two NoSQL engines, Cassandra for storing trajectories and MongoDB to store analysis results and simulation metadata. The analyses available include backbone geometries, helical analysis, NMR observables and a variety of mechanical analyses. Individual trajectories and combined meta-trajectories can be downloaded from the portal. The system is accessible through http://mmb.irbbarcelona.org/BIGNASim/. Supplementary Material is also available on-line at http://mmb.irbbarcelona.org/BIGNASim/SuppMaterial/.
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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.