mol_model_course

Workshop: Protein structure modelling in Modeller

Description

• We will obtain protein structure based on templates
• Duration: 60 minutes
• Objectives: be able to
  • Prepare protein sequences for Modeller.
  • Select a template based on sequence identity comparison.
  • Align target sequence with the template
  • Model building.
  • Model evaluation.

Jupyter notebook

• modeller.ipynb

Required software and resources

• Access to a Jupyter notebook evironment with Python 3, modeller, MDanalysis, nglview, Bio libraries
• Access to Newton cluster

Learning resources

• Tutorials
• DOPE (Discrete Optimized Protein Energy) method

Assignments

1. Build model for lactate dehydrogenase from Trichomonas vaginalis (TvLDH) based on a single template. Perfom loop refine by LoopModel, DopeLoopModel.
2. Compare plots of energy score (DOPE) for model, template, model with auto loop refine, model with Dope loop refine.

Troubleshooting

• Consult with the seminar protocol/recording
• Ask questions in Slack