Team:HKUST/Contribution
Contribution
Share instructions about VMD and scripting files on GitHub
VMD is a free molecular visualization program for modelling, visualization, and analysis of biological systems developed by the University of Illinois Urbana-Champaign. In particular, VMD provides embedded scripting languages (Python and Tcl) for the purpose of user extensibility. Here we have collated a detailed explanation of the methods our team used for MD simulation with VMD and uploaded all scripting files onto our GitHub repository. The methodology we detail for achieving our aims are versatile and hence provide a helpful resource for future iGEM teams to utilise and model their projects. Our aim is that these instructions will provide a reference point, helping future iGEM teams which wish to use VMD software to do molecular dynamics simulation.
Check out our Github here!
Alpha and Gamma subunits 3D structures prediction
Predict the 3D protein structures of alpha and gamma subunits of hagfish slime intermediate filament: Protein structure is the three-dimensional arrangement of atoms in an amino acid-chain molecule. To understand the functions of proteins at a molecular level, it is often necessary to determine their three-dimensional structure. However, the 3D protein structures of alpha and gamma subunits of hagfish slime intermediate filament haven’t been experimentally determined. Herein, with the I-TASSER server, we predicted the 3D structures of both subunits to facilitate our understanding about the properties of hagfish slime IFs. We’ve also performed structural evaluations on our predicted models with ProSA and Molprobity, and we encourage future teams to improve the modelling quality with finer tools. Our aim is to inspire future iGEMers to make good use of in-silicon tools when there is no experimentally determined 3D structure available for their target molecule.
The structure of the alpha subunit, as predicted by I-TASSER. Purple segments represent alpha helix. Registry:BBa_K1518001
The structure of the gamma subunit, as predicted by I-TASSER. Purple segments represent alpha helix. Registry:BBa_K1518000