Team:Queens Canada/Linker Software

iGEM TEAM QUEENS CANADA 2018

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COLLAPSE NAVIGATION

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• Project
  • Overview
  • Background
• Laboratory
  • Overview
  • Design
  • Experiments
  • Results
  • Improve
  • Parts
  • Safety
  • Notebook
• Modelling
  • Overview
  • Molecular Dynamic Simulations
  • Linker Development
  • Michaelis-Menten Kinetics
  • Fluid Dynamics
• Hardware
  • Overview
  • Pacifier
  • Luminometer
  • Thermistor
• Software
  • Overview
  • Luminometer
  • Linker Software
• Human Practices
  • Overview
  • Expert Interviews
  • Market Analysis
  • Education & Engagement
  • Collaborations
  • InterLab
• QGEM
  • Team
  • Attributions
  • Sponsors
  • Entrepreneurship

Linker Dynamics (Abigael)

The software being developed is designed to connect two selected points on the molecule by finding the shortest path that connects them without interfering with the rest of the molecule. This is done by first finding the shortest path at a specified resolution using an extended version of Dijkstra’s Algorithm. After the shortest path has been found linkers are designed to suit the path found. The method used to generate the linkers has yet to been determined. This software will be usable through the PyMOL software to account for visual representation and interaction with the molecule of choice.

Eric's Latex files (to insert)

We determined that the linkers between the GR-LBD and the inteins halves would need to be flexible as there is no direct path connecting the termini and they would require the flexibility to meet each other and produces a trans-splicing event. To determine which linker would be ideal we ran simulations of Root-mean-square deviation of atomic positions to determine optimal linker length and composition. Firstly, we chose various linker designs inspired from previous work [a,b], then the entropy equations were run on the Queen’s University Computer Cluster for seven days by Dr. Campbell.