Introduction

The Tools and Comparative Modelling practical serves as a learning exercise in which you will start to use tools required for your Mini-Projects. This page provides an overview of the methods you will use (as contained in Lecture 5: Predictive Tools) and links to servers which you will use for the practical and for the projects.

Predictive tools allow us to make predictions about the structure and function of a protein given only its sequence.

While Anfinsen's principle states that all the information necessary to encode a protein's three dimensional structure is contained in it's amino acid sequence, the rules by which this occurs are not sufficiently well understood for us to predict the 3D structure from sequence using first principles.

What do we want to know about a coding sequence of DNA?

1. The protein sequence it codes for
2. The function of that protein
3. Which amino acids are involved in the function and how they mediate those roles?
4. The cellular location of the protein e.g. is it membrane bound?

Stages to gaining that information:

1. Sequence matches with proteins for which structure and/or functional information is known
2. Secondary structure of the protein
3. The 3D (tertiary) structure of the protein

i.e. The ultimate goal is