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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.

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1. L-lactate dehydrogenase [Trichomonas vaginalis]
GenBank: AAC72735.1
GenPept Identical Proteins Graphics
>AAC72735.1 L-lactate dehydrogenase [Trichomonas vaginalis]
MSEAAHVLITGAAGQIGYILSHWIASGELYGDRQVYLHLLDIPPAMNRLTALTMELEDCAFPHLAGFVAT
TDPKAAFKDIDCAFLVASMPLKPGQVRADLISSNSVIFKNTGEYLSKWAKPSVKVLVIGNPDNTNCEIAM
LHAKNLKPENFSSLSMLDQNRAYYEVASKLGVDVKDVHDIIVWGNHGESMVADLTQATFTKEGKTQKVVD...

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