Mathematical simulations in biomedical sciences

Lecturer:

Tutor:

Supervisor:

Department of Natural Sciences

Synopsis:

Basic ideas and concepts of the computer usage in biological, biochemical a medicinal research and laboratory practice. The focus is on the genetics and biochemical protein interactions. Structure and types of the information received from molecular biology and biochemistry. Simple and complex alignment of DNA, RNA and protein sequences. Scoring functions. Advanced statistical methods. Modeling of the protein-environment interaction.

Requirements:

Active participation in th tutorials. The exam consists of a written and an oral parts. Half of the points of the written part is necessary to pass the exam.

Syllabus of lectures:

1.Introduction I.

2.Introduction II.

3.Sequence alignment

4.The basics of the mathematical probability functions

5.Scoring functions and programs

6.Structural alignment

7.Databases

8.Data interpretation

9.Protein modeling I. - Mathematical background

10.Protein modeling II. - practical part

11.Protein modeling III. - protein-solvent interaction

12.Protein modeling IV. - protein-substrate interaction

13.Practical training

Syllabus of tutorials:

The aim of this subject is to provide basic ideas and concepts of the computer usage in biological, biochemical a medicinal research and laboratory practice. The focus is on the genetics and biochemical protein interactions. Structure and types of the information received from molecular biology and biochemistry. Simple and complex alignment of DNA, RNA and protein sequences. Scoring functions. Advanced statistical methods. Modeling of the protein-environment interaction.

Study Objective:

The aim of this subject is to provide basic ideas and concepts of the computer usage in biological, biochemical a medicinal research and laboratory practice. The focus is on the genetics and biochemical protein interactions. Structure and types of the information received from molecular biology and biochemistry. Simple and complex alignment of DNA, RNA and protein sequences. Scoring functions. Advanced statistical methods. Modeling of the protein-environment interaction

Study materials:

1.Gribskov, M., Devereux, J. (1991). Sequence Analysis Primer. New York: Stockton Press.

2.Avi Silberschatz , Henry F. Korth, S. Sudarshan (2005) Database System Concepts, Fifth Edition: McGraw-Hill

3.J. Andrew McCammon, Stephen C. Harvey (2004) Dynamics of Proteins and Nucleic Acids: Cambridge University Press

Note:

Further information:

No time-table has been prepared for this course

The course is a part of the following study plans: