UNIVERSITY OF THE WESTERN CAPE
MODULE DESCRIPTOR: NEW MODULES
Version
Name of new module
Structural Bioinformatics
Rationale for introduction of new module
Structural bioinformatics deals with aspects of structural biology that are best handled by computer. The topics
range from databases of known structures, data handling, structure computation, modelling
Programme (s) in which new module will be offered
Programme
Faculty (if also prescribed for programmes not in your
faculty, please indicate date of agreement)
PG Diploma in
Structural
Biology
UWC Faculty of Natural Sciences
UCT Science Faculty
Home Department
Molecular and Cell Biology, UCT
Module description (Header)
Structural Bioinformatics
Generic module name
Alpha-numeric code
Module numeric code (if
available)
Structural Biology
STB705
Core/ Elective
Core
Credit Value
Duration
Module Type
Level
Main Outcomes
10
3 weeks
P
8
The ability to:
* obtain structural insights from biomolecular databases
* predict protein secondary structure
* predict the three dimensional structure of proteins which
have homologue whose structure is known.
* display proteins and other biomolecules
* display and interpret experimental structural data
* dock protein models into experimentally determined maps
Main Content
Introduction
The observed structure of proteins - amino acids, alpha
helices, beta sheets, beta bends
The forces that shape proteins - vdW, charge interactions,
hydrogen bonds (modelled as charge interactions), the
hydrophobic effect
Force field modelling
The concept of energy and potential functions - what the
physically real ones look like and empirical fudges. The
limitations of our models and how we believe we could
improve things by going to QM
Energy minimization, MD and Monte-Carlo. Normal Modes.
Emipirical prediction
Chou-Fasman
Psipred
PSST's
Secondary structure databases, protein classification
Structural alignment
Fugue
GenThreader
Fusion Ideas
Modeller
The ideas of David Baker
Bringing in Experimental Data
The nature of data from NMR,EM and Xray crystallography
Maps and resolution
Combining modelling with experimental data
Docking
Refinement - Refmac, CNS, real-space refinemnt
Matching constraints in NMR
Impact on proteomics - protein protein docking
Impact on drug discovery - databases of small molecules active site docking - cavity fitting - in silico screening
Computational Strategies
Representations and interactive tools
PyMol
Chimera
O
VMD
Pre-requisites
Co-requisites
Prohibited Combinations
Breakdown of Learning Time
None
None
Hours
(example)
Contact with lecturer / tutor:
Assignments & tasks:
Tests & examinations:
Practicals:
Selfstudy
Other: Please specify
Total Learning Time
55
15
0
20
10
0
100
Methods of Student
Assessment
Students will be required to submit a practical write up and
complete a assignment.
Assignments – 100%