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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, got the simulations and analyzed the results.
We picked the 1S12 dataset which represents the Crystal structure of TM1457 from Thermotoga maritima and ran its structure prediction calculations. We used the computer terminal to run the protein with nstruct set to 10 (score.fsc, approximately 45 minutes 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_00000003.pdb (energy: -118,114) and the lowest rms model is S_00000010.pdb (rms: 10,939)
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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?
The lowest energy value for the nstruct=10 simulation was -118,114 (rms=12,225) and corresponded to S_00000003.pdb
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.
The lowest rms model for the nstruct=10 simulation was 10,939 and corresponded to S_00000010.pdb.
The objective of this assignment was to run the Rosetta protein structure prediction simulations and analyze the results. The idea was 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. We picked one of the five test cases in the homework folder and ran structure prediction calculations. The native structure of all the five test cases has already been solved. So, you could compare our output against the correct answer.
We compared the structures of the lowest energy model obtained to the native using RCSB Viewer (http://www.rcsb.org/pdb/explore/jmol.do?structureId=4HHB&opt=3&bionumber=1)
They looked very different since we only ran 10 models, we weren’t able to run more models because of the low RAM power of the computer available. Generating more models will lead to a better prediction, and a structure more similar to the native.
View of simulation structure of S_00000003.pdb (lowest energy value, nstruct = 10)
View of Crystal Structure of 1S12
View of lowest rms value simulation of S_00000010.pdb (nstruct = 10)
View of Crystal Structure of 1S12
We compared the structures of the lowest rms model obtained to the native using RCSB Viewer (http://www.rcsb.org/pdb/explore/jmol.do?structureId=4HHB&opt=3&bionumber=1)