q1:
Load the trajectory file in VMD ( the files you need are in a compressed folder on blackboard).
Calculate the RMSD, contact map along the trajectory time. Explain what the RMSD, contact map are, and what information they provide. (10 points)
Calculate the distance between residue 56 atom O and residue 290 atom CA. (5 points)
Calculate the Phi and Psi angles of residue 299 along the trajectory time. (10 points)
q2: Go to the PDB databank and download the structure of 2HHB.
Show in details the steps you need to take to prepare your protein for Molecular Dynamics Simulations. Provide snapshots, save all in a word document
q3: Use MODELLER to generate an initial structural model for the following target sequence:
PIVDSGSVAPLSAAEKTKIRSAWAPVYSNYETSGVDILVKFFTSTPAAQEFFPKFKGMTSADQLKKSADVRWHAERIINA
VNDAVASMDDTEKMSMKLRDLSGKHAKSFQVDPQYFKVLAAVIADTVAAGDAGFEKLMSMICILLRSAY
In your search, use homologous sequences with known structures for protein in humans (taxid: 9606).
Follow the steps you have learned to generate the best models.
Use the files in the ModelScripts folder to run modeller, and document carefully your input and output results in a separate word document.
To test your model compare it with the chain A of PDB code 1UC3.
Answer questions in complete sentences wherever possible, and insert screenshots when necessary in a word document
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