Protein-Protein Interactions

Tools and Approaches

Slides:
https://rbvi.github.io/chimera-tutorials/presentations/ppi-tools-2.html#/

John "Scooter" Morris

Max Planck Institute for Biology of Ageing
28 November 2017

Today's Agenda

Time	Topic
09:00 - 10:30	Protein-protein interactions at the molecular level - I
10:30 - 11:00	Break
11:00 - 12:30	Introduction to UCSF Chimera
12:30 - 13:30	Lunch
13:30 - 15:00	Comparative Modeling with UCSF Chimera
15:00 - 15:30	Break
15:30 - 17:00	Work on your own data

Sources of molecular PPI data Molecular Visualization Introduction to UCSF Chimera Hands-on: Comparative Modeling ChimeraX/Project

UCSF Chimera Demo

HIV Demo

Sources of molecular PPI data Molecular Visualization Introduction to UCSF Chimera Hands-on: Comparative Modeling ChimeraX/Project

Hands-on

Chimera→Help→Tutorials

Sources of molecular PPI data Molecular Visualization Introduction to UCSF Chimera Hands-on: Comparative Modeling ChimeraX/Project

Project

Feel free to work with your own data (using either Cytoscape or UCSF Chimera). If you didn't bring any data of your own to work on, here is a project to try:

BRCA1 and BRCA2 are proteins that are strongly associated with the increased risk of breast cancer in women when they have certain mutations. Much is known about these proteins and their function in the DNA damage response/DNA repair pathways. Similarly the tumor suppressor protein TP53 is known to be mutated in many cancers. For this project, explore the protein-protein interactions linking one of the two BRCA genes and TP53 from both a network and structural perspective. Based on your analysis, propose a mechanism for the functional impact of BRCA mutations. Include both network and structural information in your results.