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Jožef Stefan
International
Postgraduate School

Jamova 39
SI-1000 Ljubljana
Slovenia

Phone: +386 1 477 31 00
Fax: +386 1 477 31 10
Email: info@mps.si

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Course Description

Analysis and Prediction of 3D Protein Structure

Program

Nanosciences and Nanotechnologies, third-level study programme

Lecturers:

prof. dr. Andrej Šali
prof. dr. Veronika Stoka

Goals:

Students learn the basics of bioinformatics, protein structures, and become acquainted with methods for their analysis and prediction.

Content:

Within this course, protein structures will be researched from two basic aspects: the laws of physics and the theory of evolution. From the aspect of physics, the native structure of proteins is the result of forces acting on the atoms of protein and solvent in the process of its folding, while from the biological aspect the native structure of protein is the result of evolution. Both basic principles also form the foundation for the protein structure prediction methods. The first, i.e., de novo or ab initio methods attempt to predict the structure of proteins from their sequence alone, not referring to the similarity at the level of folding between the modelled protein sequence and known structures. The second class of methods, which includes comparative modelling, is based on the similarity between the major part of the sequence of modelled protein and at least one known structure.
We will research the nature of forces controlling the formation of a particular protein structure and certain aspects of the protein folding process, compare protein sequences, and protein structures, model proteins in many different ways, and research structural genomics and the possibilities for predicting the functions of proteins by predicting their structure.

Course literature:

Pieper, U., Eswar, N., Stuart, A. C., Ilyin, V. A., Sali, A. " MODBASE, a database of annotated comparative protein structure models" (2002) Nucleic Acids Research, 30, 255-259.

D. Baker, A. Sali. Protein structure prediction and structural genomics. Science 294, 93-96, 2001

Martí-Renom, M. A., Stuart, A., Fiser, A., Sánchez, R., Melo, F., Sali, A. " Comparative protein structure modeling of genes and genomes" (2000) Annu. Rev. Biophys. Biomol. Struct. 29, 291-325.

Carl-Ivar Branden and John Tooze. Introduction to Protein Structure, Garland Publishing, 2nd edition, 1999.

Developing Bioinformatics Computer Skills (2001) C. Gibas, P. Jambeck, O'Reilly & Associates, ISBN 1565926641

Bioinformatics: A Practical Guide to the Analysis of Gene and Proteins (2001) 2nd edition, A. D. Baxevanis & B. F. F. Quellette, ed., John Wiley & Sons, ISBN 0471383910.

Bioinformatics Basics Applications in Biological Science and Medicine (1999), H. H: Rashidi, L. K. Buehler, CRC Press: ISBN
0849323754.

Significant publications and references:

M. A. Marti-Renom, B. Yerkovich, A. Sali. " Comparative protein structure prediction" , Current Protocols in Protein Science 1, 2.9.1-2.9.22, 2002.

M. R. Chance, A. R. Bresnick, S. K. Burley, J. S. Jiang, C. D. Lima, A. Sali, S. C. Almo, J. B. Bonanno, J. A. Buglino, S. Boulton, H. Chen, N. Eswar, G. He, R. Huang, V. Ilyin, L. McMahan, U. Pieper, S. Ray, M. Vidal, L. K. Wang. " Structural Genomics: A pipeline for providing structures for the biologist" Protein Science 11, 723-738, 2002.

A. Fiser, A. Sali. " MODELLER: generation and refinement of homology models" In: Methods in Enzymology. Eds: C. W. Carter, R. M. Sweet. Academic Press, San Diego, vol. 374, 463-493, 2003.

D. Baker, A. Sali. " Protein structure prediction and structural genomics" Science 294, 93-96, 2001.

A. Fiser, M. Feig, C. L. Brooks III, A. Sali. " Evolution and physics in comparative protein structure modeling" Accounts of Chemical Research, 35, 413-421, 2002.

Examination:

• seminar and oral exam

Students obligations:

• seminar and oral exam

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