GENE 433 Laboratory Manual

This site contains the lab manual for GENE 433 Molecular Modeling and Protein Structure Prediction.

Warning

Links and some contents are currently being reviewed. The course assistant will be a couple weeks ahead of you to ensure all links work correctly and the content is up to date.

Contents

• Pre-Lab 1 - Biological Data and Molecular Geometry
• Pre-Lab 2 - Bioinformatics Environment, Workflow, and Reproducibility
• Lab 1 - Usage of web-sites and web-based tools
• Lab 2 - Secondary Structure Prediction
• Lab 3 - PDB and PDBsum
• Lab 4 - Jmol
• Lab 5 - UCSF Chimera
• Lab 6 - Chimera Tutorials
• Lab 7 - Swiss-Pdb Viewer
• Lab 8 - Sequence Alignment
• Lab 9 - Protein Structure Prediction Using AlphaFold
• Lab 10 - Homology Modeling
• Lab 11 - Docking and Drug Discovery
• Term Project