University of Surrey - Guildford
Registry
  
 

  
 
Registry > Provisional Module Catalogue - UNDER CONSTRUCTION & SUBJECT TO CHANGE
View Module List by A.O.U. and Level  Alphabetical Module Code List  Alphabetical Module Title List  Alphabetical Old Short Name List  View Menu 
2011/2 Provisional Module Catalogue - UNDER CONSTRUCTION & SUBJECT TO CHANGE
 Module Code: CHE2032 Module Title: COMPUTER MODELLING OF DRUGS AND BIOMOLECULES
Module Provider: Chemical Sciences Short Name: CHE2032
Level: HE2 Module Co-ordinator: HOWLIN BJ Dr (Chem Science)
Number of credits: 15 Number of ECTS credits: 7.5
 
Module Availability
Semester Two
Assessment Pattern
Coursework (100%)
Module Overview
Prerequisites/Co-requisites
Module Aims
  • To introduce students to the techniques of molecular modelling applied to both small molecules and proteins and the use of a range of databases in these studies.
  • To examine simple quantum mechanical calculations.
  • To gain practical experience in homology modelling of proteins.
  • To introduce the concepts behind chemoinformatics.
  • To describe the representation of structural and chemical data.
  • To introduce the use of 2-dimensional reduction, for specifying chemical structures.
  • To study the use of databases to store and retrieve structural and chemical data.
Learning Outcomes

On successful completion the student will, or will be able to:

 

·         be familiar with the wide range of modelling techniques as a precursor to the Industrial Research Year and beyond

 

·         have an understanding of the nature of a relational database;

 

·         have an understanding of  how chemical data can be represented in a relational database;

 

·         have an appreciation of how to carry out practical projects requiring teamwork and initiative to use the most advanced methods to store and retrieve 3-dimensional data in a database and to display it in a variety of ways.

 

·         understand the science behind how to reduce a 3-dimensional structure to a 2-D format.

 

·         have an understanding of how to carry out QSAR analysis on pharmaceutical compounds.

 
Module Content

BJH         

 

1-7

 

Introduction to molecular modelling and computational chemistry.

 

Simple theory of molecular mechanics and molecular orbital calculations. Energy expressions and minimisation techniques.

 

Deriving molecular mechanics parameters.

 

Small Molecule Modelling.

 

Practical applications using MOE, ARGUSLAB and GAUSSIAN on PCs with GAUSSVIEW.

 

Conformations in molecules and conformational analysis.

 

Using GAUSSIAN to predict and animate IR and NMR spectra of simple molecules

 

ACT

 

8-12

 

Protein Modelling and Databases

 

Introduction to protein three-dimensional structure covering aminoacids, codes for aminoacids, sequence analysis, primary, secondary, tertiary and quaternary structure.

 

The Brookhaven Database for protein X-ray structures and using the Web Browser.

 

Protein structure prediction, use of artificial intelligence (the EMBL Predict-Protein programme) and other internet resources.

 

The use of DEEPVIEW for visualising structures.

 

BJH

 

13-33

 

Introduction to chemoinformatics, what it is, what it can do.

 

3D-2D reduction- the SMILES string

 

Introduction to the DAYLIGHT databases

 

Use of SMILES to retrieve structures

 

SMIRKS, encoding reactivity in databases

 

Simple combinatorial chemistry exercise using SMILES and SMIRKS

 

Does it exist? Validating results

 

Lipinski’s rule of Five, LogP and CLOGP

 

QSAR, what it is and what it is used for

 

Practical example of QSAR using ACE inhibitors

 

QSAR with MOE

 

QSAR with DAYLIGHT

 

Multiple Linear Regression

 

The Cambridge Crystallographic Database.

 

Searching and retrieving structural data from the CCDB

 

Use of the Cambridge database in informatics.

 
Methods of Teaching/Learning
The nature of the topic is such that delivery is best via workshops and practical sessions. Students will gain experience with a wide range of software packages and learn to model small molecules and proteins with a view to deepening their understanding of three dimensional structure and how shape influences drug design.  A ‘Hands on’ workshop approach will be adopted throughout with classes held in the computing laboratory
Selected Texts/Journals

Recommended:

 

Leach, A.R,: (2001), Molecular Modelling, Principles and Applications, 2nd Edn., Longman

 

Leach, A.R. and Gillett, V.J., (2003), An Introduction to Cheminformatics, Kluwer Academic Publishers.

 

 

 
Last Updated
21 April 2011