Module 6: Homology Modeling
Assignment #1
Structure Prediction and Molecular Graphics
Task: Retrieve the sequence for lactate dehydrogenase from Trichomonas vaginalis(TvLDH, AAC72735.1) from the server of your choice in FASTA format.

1.Use the SWISS-MODEL server to identify the template with the lowest resolution and highest sequence identity. Indicate the PDB ID, % sequence identity, sequence similarity, and resolution.
2.Build a model using the SWISS-MODEL server, based on the selected template. Indicate the predicted local similarity to target (local model quality: DOPE, Discrete Optimized Protein Energy) and the overall model quality (Z-score) for the generated model. In addition, show an image of the generated model and model-template alignment.
3.Describe the QMEAN score for the model. How good is the generated model based on this parameter?
4.Save the generated model as a PDB file.
Modeller
1.Use the MODELLER file (compare.log) to identify the template with the lowest resolution and highest sequence identity. Indicate the PDB ID, % sequence identity, sequence similarity, and resolution.
2.Show the alignment in MODELLER (align2d.log), based on the selected template. 3.Use the DOPE scores (model_single.log) to select the best generated model. Open the PDB file corresponding to the structure withthe best DOPE score and identify any defining secondary and tertiary structural elements.
4.Use the ProSA server to verify the model by indicating the predicted local similarity to target (local model quality: DOPE, Discrete Optimized Protein Energy) and the overall model quality (Z-score) for the generated model. In addition, show an image of the generated model.
Assignment #2
Comparison of computer-vs. user-generated model
1.Use the SuperPoseProtein Comparison Tool to align the two custom PDB files.
2.Provide the following information:
•Images of the superimposed PDB file in the molecular visualization software of your choice
•Difference distance matrix
•Sequence alignment
•RMSD report
What does this information tell you about the agreement between the two structures?

Module 6: Homology Modeling Assignment #1 Structure Prediction a...