Protein Interactions

Introduction

The interactions among proteins and other molecules are of fundamental importance for the many biological processes that take place into living cells. Ligands can be other proteins, but also peptides, nucleic acids or small molecules. Here, we will study protein interactions from two main different points of view:

1. Single interactions at the molecular/atomic level, rather than the entire biological system (cell, tissue or organism);
2. Protein interaction networks;
3. Interaction of proteins with small molecules and the principle of drug design.

Learning Outcomes

These materials will enable successful learners to be able to:

1. describe the molecular/atomic forces at play in protein interactions
2. discuss principles, challenges, and limitations of protein-protein docking
3. run ClusPro, a web server for protein-protein docking
4. analyse ClusPro results
5. critically use PPI main databases
6. describe protein-protein interaction (PPI) networks and their properties
7. carry out a topological analyisis of PPI networks using Cytoscape
8. explain what biological information we can extract from PPI
9. describe the process of drug development
10. explain what is drug design and how it works
11. explore DrugBank and ChEMBL

Target Audience

• Learners who want to gain foundational knowledge, skills and modes of reasoning that are essential to the understanding of PPIs and their study

Prerequisites

• Basic knowledge of cell and molecular biology
• Skilled in the use of computers