The objective of the homework is to run the Rosetta protein structure prediction simulations and analyze the results.The idea is to get an understanding of how computational protein modeling works, looking at protein structures using a viewer (PyMol or Chimera or Rasmol) and making sense of the squiggles and wiggles. You'll also hopefully appreciate the computing power needed for biomolecular simulations. You'll pick one of the five test cases in the homework folder and run structure prediction calculations. The native structure of all the five test cases has already been solved. So, you can compare your output against the correct answer.

​

1. Plot the score (or energy) vs rms plot. Rms stands for root mean square deviation. These are two columns in the score.fsc file. Compare that with the energy vs rms plots I showed in my slides.

​

​

​

​

​

​

​

​

​

​

​

​

We ran the Rossetta protein structure in Linux (server 128 GB RAM), got the simulations and analyzed the results.

We picked the 1S12 dataset which represents the Crystal structure of TM1457 from Thermotoga maritimaand ran its structure prediction calculations. We used the computer terminal to run the protein with 300 models (score.fsc “attach”, approximately 7 hours run time) We compared the results against the correct answer already given on the folder.

We opened score.fsc as an excel file. The score.fsc output files have a lot of data yet we only want to work with the scores and rms columns.

The lowest energy model is S_00000060.pdb (energy: -78.759) and the lowest rms model is S_00000091.pdb (rms: 4.805)

​

​

​

​

​

2. Pick the lowest energy model and structurally compare it to the native. How close is it to the native? If its different, what parts did the computer program get wrong? You'll have to compare the structures using a Viewer like pymol or chimera or rasmol.

​

​

​

​

​

​

​

​

​

​

​

​

​

​

​

 

 

 

 

 

 

 

3. Pick the lowest rms model and structurally compare it to the native. How close is it to the native? If its different, how is it different? Remember that in a blind case, we will not have the benefit of an rms column.