Thomas C. Bishop(PI)
Ran Sun
TMB-iBIOMES 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.
Dr. Bishop's research interests are in the area of theoretical and computational molecular biology, with a particular emphasis in molecular modeling and molecular dynamics simulations of proteins and DNA. The current focus is developing a multiscale model of DNA, nucleosomes and chromatin. The structure and dynamics of DNA and chromatin are being modeled by a combination of molecular dynamics and mathematical modeling techniques. The goal of this research is to develop an understanding of how local events, such as DNA binding, affect the global structure and dynamics of DNA and chromatin. For this purpose, all atom molecular dynamics simulations are used to model DNA and protein-DNA interactions in solution. The results are analyzed to characterize the effects of the protein on the conformation and dynamics of the DNA, including DNA bending, twisting, and stretching. This information is then included in a model of DNA based on the theory of elastic rods that predicts how local distortions of DNA alter the structure and dynamics of DNA and chromatin on longer length scales. The elastic rod model being developed thus provides a rigorous mathematical basis for analyzing how protein-DNA interactions and DNA sequence specific properties orchestrate cellular processes such as gene regulation.