What is the TMB Library?

DOI: 10.1021/acs.jcim.9b00252

Bishop’s TMB library presents over 20 microseconds of all atom molecular dynamics simulations for over 500 different realizations of the nucleosome. For... every simulation the following files are presented: initial Amber formatted parameter and topology files (*.parm) and coordinate files (*.crd) with and without solvent (sys.* and nowat.*, respectively). namd2 formatted configuration (*.conf) and output files (*.log), dewatered DCD trajectory files (*.dcd), RMSD trajectory data (*.png and *.dat), and inter and intra basepair stacking and step parameters (*.nastruct.dat). Closely related simulations are grouped together and a summary of DNA helical parameter data and Cartesian coordinate RMSD data is provided. All of this data can be navigated in a file browser format or downloaded directly with command line tools or accessed via an iBIOMES Lite instance.

Simulation


ACGT

This system is a set of controls designed to represent all possible DNA sequence variants at each of the 146 dimer step locations in an octasome.

MMTV-NucA

The MMTV is known to position six nucleosomes, referred to as nucleosomes A to F. Our systems were modeled by docking the relevant MMTV sequence to 1KX5.

NUC146

NUC146 represents a set of simulations based on x-ray structures, 2CV5, with the mutation to the histone for different species.

SIN-Mutants

The systems were built manually and represent single-point mutations associated with disruption of the SIN complex.