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Syllabus for

Academic year
TDA506 - Structural bioinformatics
 
Owner: BIMAS
5,0 Credits (ECTS 7,5)
Grading: TH - Five, Four, Three, Not passed
Level: C
Department: 37 - COMPUTER SCIENCE AND ENGINEERING


Teaching language: English

Course module   Credit distribution   Examination dates
Sp1 Sp2 Sp3 Sp4 No Sp
0105 Written and oral assignments 5,0 c Grading: TH   5,0 c    

In programs

TKBIA BIOENGINEERING, Year 4 (elective)
BIMAS MSc PROGRAMME IN BIOINFORMATICS, Year 1 (compulsory)
TM Teknisk matematik, Year 2 (elective)
TITEA SOFTWARE ENGINEERING - Software development and management, Year 4 (elective)
TITEA SOFTWARE ENGINEERING - Data communication, Year 4 (elective)
TITEA SOFTWARE ENGINEERING - Embedded systems, Year 4 (elective)
TITEA SOFTWARE ENGINEERING - Interaction design, Year 4 (elective)
TITEA SOFTWARE ENGINEERING - Interactive simulations, Year 4 (elective)
TITEA SOFTWARE ENGINEERING - Bioinformatics, Year 4 (compulsory)

Examiner:

Bitr professor  Graham Kemp


Replaces

TDA505   Three-dimensional structure


Eligibility:

For single subject courses within Chalmers programmes the same eligibility requirements apply, as to the programme(s) that the course is part of.

Course specific prerequisites

The material on protein structure covered in "Introduction to bioinformatics",
or similar knowledge about protein structure from other courses, is assumed.

Essential: an introductory programming course.
Desirable: material on data structures.
Desirable: programming skills in C. However, knowledge of Java or another
procedural programming language should be sufficient to enable students to
read and modify example C programs in practical classes.

Aim

In this course we consider "structural bioinformatics" to be the development
and application of computational methods (i) to analyse and predict the
conformations of biological macromolecules and (ii) to study relationships
between macromolecular structure and function. Protein molecules will be
in focus, but other biological molecules will also be studied.

The aims of this course are:

* to present some of the computational challenges in structural biology;
* to describe computational methods for analysing and predicting
macromolecular conformations and interactions;
* to give practice in programming techniques for structural bioinformatics.
* to give practice in the use of molecular graphics and modelling software;
* to emphasise the relationship between macromolecular shape and function.

Goal

At the end of this course, students should:

* be familiar with algorithms and data collections that are central to
structural bioinformatics;
* understand computational methods used in protein modelling, docking,
and other areas of structural bioinformatics;
* be able to write programs to analyse protein structure data;
* be able to use software packages for macromolecular structure analysis,
modelling and docking;
* be aware of applications of structural bioinformatics that are directed
towards understanding and predicting biological function.

Content

three-dimensional structures of biological macromolecules;
contact maps and distance maps;
domain assignment;
homogeneous transformation matrices;
structure superposition;
structure comparison;
comparative protein modelling;
protein fold recognition;
Monte Carlo methods and simulated annealing;
ab initio protein structure prediction;
protein shape representation;
protein-ligand interactions and applications in drug design;
conformational analysis;
protein-protein docking;
modelling transmembrane proteins, carbohydrates and RNA;
experimental protein structure determination using nuclear magnetic
resonance (NMR) and X-ray crystallography;
applications of structural bioinformatics.

Organisation

Lectures and practicals, including the use of molecular modelling software.

Literature

Lecture handouts; web-based resources; selected research articles.

"Structural Bioinformatics" edited by Philip E. Bourne and Helge Weissig
(2003, published by Wiley-Liss, ISBN 0-471-20199-5) is suggested for
consultation, but is not a required text for this course.

Examination

TBC, but in the "Three-dimensional Structure" course we currently use
a series of individual assignments.


Page manager Published: Thu 03 Nov 2022.