TMB-iBIOMES: An iBIOMES-Lite Database of Nucleosome Trajectories and Meta-Analysis

Abstract

<div>Here we introduce our TMB-iBIOMES database which serves as both a reference for future comparative, on-demand simulations of nucleosomes and a demonstration of iBIOMES-Lite as a tool for managing a laboratory's simulation inventory. TMB-iBIOMES contains over 20 microseconds of all atom molecular dynamics simulations for over 500 different realizations of the nucleosome. For every simulation, the original input, output, de-watered trajectories, RMSD, and DNA helical parameter data are provided. Closely related simulations are grouped together, and a meta-analysis of each group is provided. The data can be navigated in a file browser format or downloaded directly with command line tools. Collectively the simulations provide a novel view of nucleosomal DNA. Compared to DNA free in solution, DNA on the nucleosome is not highly deformed or tightly restricted as determined by DNA helical parameter analysis. The overall conformation is restricted to a specific left-handed super helix, but the range of conformations explored by individual base pairs is larger than that observed for DNA free in solution. </div>

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“…The BioExcel CoE and the ELIXIR European Initiative have defined a prototype of EDAM ontologies for metadata of MD simulations. 148 This should be extended and refined to be adopted by already existing 10 , 149 , 150 , 151 , 152 , 153 , 154 , 155 or new simulation databases. Some recent databases such as BigNASim already implement an ontology metadata 154 which helps to classify trajectories, favoring then meta‐analysis and the detection of artefactual simulations.…”

“…More recent efforts have been focused on specific families of proteins of special importance, such as GPCRmd that includes trajectories of G‐protein coupled receptors, MemProtMD, 156 which contains simulations on 3500 membrane proteins in realistic membrane environments, or TMB‐iBIOMES that includes hundreds of nucleosome trajectories. 152 A few databases are focused on small molecules with potential biomedical or biomolecular impact; an example is Cyclo‐lib 153 which is focused on cyclodextrins, or BCE, 155 which contains classical trajectories and quantum structural data on small drugs. Finally, BigNASim 154 is, to our knowledge, the only database focused on nucleic acids simulations, and contains hundreds of simulations including the latest ones obtained by the ABC consortium.…”