Ribosome Builder: A software project to simulate the ribosome

William Knight, Walter Hill, J. Stephen Lodmell

Research output: Contribution to journalArticlepeer-review

Abstract

The Ribosome Builder is a software project that provides tools and techniques to create dynamic models of macromolecular systems from the rapidly growing numbers of atomic structural models. It includes a computer program that allows the user to assemble the multiple molecular components within a 3D space and to define the hypothetical interactions of these components with the initial goal of understanding protein translation at an atomic level of detail. The program employs a simplified molecular dynamics forcefield that can simulate the long time-scale events, such as docking of translation factors and mRNA translocation. An embedded scripting language and Application Programming Interface (API) enable the creation of Steered Molecular Dynamics (SMD) simulations through the programmable application of external forces and torques on atoms and bonds. A graphical interface is provided for displaying and interacting with models, recording movies of molecular dynamics movements, and creating annotated 3D simulations of complex macromolecular events. Initial applications of the project include simulation of tetraloop folding, docking of an mRNA on the 30S subunit and a schematic simulation of the translation elongation cycle. The program is an open source project released under the GNU public license.

Original languageEnglish
Pages (from-to)163-174
Number of pages12
JournalComputational Biology and Chemistry
Volume29
Issue number2
DOIs
StatePublished - Apr 2005

Keywords

  • Macromolecular simulation
  • Ribosomal translation
  • Ribosome modeling
  • RNA
  • Steered molecular dynamics

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