Projects
Bioen 488 Projects (Pick One)
Bioen 588 Project Ideas
Constraints to consider when designing your project, keep your system simple
- General protein properties
- <250 amino acids
- PDB structure with better than 3 Å resolution
- No cofactors, metals, mixed solvents, nucleic acids
- Not a membrane protein
- Monomers are preferred but if you want to include more than one molecule see the link and keep system <250 residues ilmm multimer setup
- Things you can do with ilmm
- Change the temperature
- Raise/Lower the pH
- Measure RMSD, RMSF, secondary structure, contacts, internal distances, etc, etc
- Things you can do with Rosetta
- Rotamer optimization to change sequence with a fixed backbone
- Sidechain and backbone energy minimization
- Loop modeling/relaxation, etc etc