Protein Bioinformatics

• Credit value: 30 credits at Level 7
• Convenor and tutor: Clare Sansom
• Assessment: a 1.5-hour examination (66%) and coursework (34%)

Bioinformatics is at the heart of modern molecular biosciences. The term covers any use of computational sciences to analyse biological data, particularly molecular data. Without it, structural biology would have merely generated a mountain of uninterpretable data. This module will introduce you to a range of techniques that are regularly used to analyse protein sequences and structures, and will explain how these techniques complement experimental structural biology and its application in drug discovery.

Indicative module syllabus

• Introduction and sequence alignment
• Advanced sequence alignment and protein family detection
• Analysis of protein structures and function prediction
• Modelling molecular structures
• Protein structure prediction
• Docking, cheminformatics and drug design

By the end of this module, you will be able to:

• discuss the relationships between protein sequence, structure and function and how bioinformatics tools are used to interpret these relationships
• explain how principles of protein sequence similarity are used in pairwise and multiple sequence alignment, in BLAST, and in other methods of searching databases with protein sequences; make use of alignment and database searching programs
• appreciate the detailed data held in a PDB file and understand the limits of its precision and accuracy
• explain the hierarchy of protein structure and how each level is built up from the one below, including interatomic interactions, force fields and basic ideas about protein folding
• appraise the appropriateness of different methods for predicting protein structure from sequence; describe how these methods work and be able to interpret their results
• describe how proteins interact with each other and with small molecules such as ligands and enzyme inhibitors, and explain how these interactions can be modelled mathematically
• use molecular modelling software such as Chimera to run molecular simulations and interpret results
• explain how each of the methods discussed in the module can be used in the drug design and discovery process.