Toward a Whole-Cell Model of Ribosome Biogenesis: Kinetic Modeling of SSU Assembly
Tyler M. Earnest1,2, Jonathan Lai3, Ke Chen3,4, Michael J. Hallock5,
James R. Williamson6,7,8, Zaida Luthey-Schulten1,2,3,*
1Center for the Physics of Living Cells, 2Department of Physics, and
3Department of Chemistry, University of Illinois, Urbana, Illinois;
4Department of Bioengineering, University of California, San Diego, La Jolla,
California; and 5School of Chemical Sciences, University of Illinois,
Urbana, Illinois; 6Department of Integrative Structural and Computational
Biology, 7Department of Chemistry, and 8Skaggs Institute for Chemical
Biology, Scripps Research Institute, La Jolla, California, *Correspondence
to zan@illinois.edu.
doi: 10.1016/j.bpj.2015.07.030
Archive of all files
Readme file for models
SBML files describing the in vitro assembly model
Lattice Microbes 2.2.1 input file describing the in vivo biogenesis model
Lattice Microbes
Acknowledgements
This work is supported by National Science foundation grants PHY-1026550 and
MCB-1244570 and the Department of Energy grant ORNL 4000134575 and it is part
of the Blue Waters sustained-petascale computing project, which is supported
byt he National Science Foundation (awards OCI-0725070 and ACI-1238993) and the
state of Illinois. Blue Waters is a joint effort of the University of Illinois
at Urbana-Chamapgin and its National Center for Supporting Applications. This
work also used the Extreme Science and Discovery Environment (XSEDE), which is
supported by National Science Foundation grant number ACI-1053575.