Module Title

Introduction to Biocomputing (74407S, 1,5 ov, advanced course, 14h)

Degree Programme:

Protein science and Biotechnology

Remarks:

• This lecture module is offered in cooperation with the Biocenter Oulu Doctoral Programme .

Lecturer(s):

• André Juffer, PhD

Pre-requisites:

• Students should have completed the Bachelor degree program
• General knowledge of proteins and protein structures
• Some feeling for physics and chemistry, in particular thermodynamics and mechanics

Co-requisites:

• Registration is mandatory.

Aims:

• To teach the basic principles of various biocomputing methodologies
• To teach students which and when to use a certain method for a given problem

Learning outcomes:

Students should be able to:

• Discuss several biocomputing techniques
• Decide which method to use under what circumstances
• Judge the quality of an analysis of a given problem by means of biocomputing techniques

Online syllabus:

An overview is given of commonly employed techniques of biocomputing to study the structural, dynamical, functional and thermodynamical properties of proteins and membranes and their interaction with other molecules. This will include a overview of computer simulation techniques such as molecular dynamics, Monte Carlo and Langevin (stochastic, Brownian) dynamics, but also concepts of continuum electrostatics, statistical thermodynamics, protein modeling techniques, protein-ligand affinity calculations and the computer simulation of the protein folding process and enzyme action. In addition, some topics in the field of Bioinformatics are discussed as well and certain commonly employed protein modeling software is introduced.

Related modules:

• Concepts of protein folding

Recommended text books:

• Leach, A.R., Molecular modelling. Principles and applications, Second edition, Prentice Hall, New York, 2001.
• Berendsen, H.J.C Simulating the physical world. Hierarchial modeling from quantum mechanics to fluid dynamics., Cambridge University Press, Cambridge, 2007.
• See also movies at Molecular Dynamics Simulations for Biomolecules with Gromacs 3.-5.2.2004

Assessment methods:

• Participants are required to present an article related to the subject of the course. The lecturer will handout these articles.
• Participants should also prepare questions for a second article which are to be discussed with the group and especially with the presenter (another participant) of that second article.
• You should not miss more than 2 lectures (one lecture is 2x45 minutes).

Lecture notes:

If you experience trouble in downloading/opening these PDF files, or printing them, please contact me.

• Introduction.
• Statistical Thermodynamics.
• Biomolecular simulation techniques.
• Electrostatic interactions.
• Coarse-grained simulation
• Ligand docking
• Prostatic Acid Phosphatase, includes quantum chemistry calculations.
• Tumor modeling.

Last modification: Tue Dec 13 14:02:18 EET 2011