Bioinformatics of Proteins

Structure, dynamics and prediction

205-1 913 1

Chen Keasar 08-6477875 keasar@cs.bgu.ac.il

The course takes place at the computer Classroom of the department of Life Sciences

http://www.cs.bgu.ac.il/~keasar/bip05

NEW !!! final grades
MOED ALEPH + grades, answers and comments
homework assignment #2
Third home work assignment
The 8th Israeli Bioinformatics symposium

Lessons

Acknowledgments

Syllabus:

Experimental determination of structure and dynamics.
Principles of protein structures:
- Structural stability.
- Folding kinetics.
molecular modeling
- Energy functions
- Energy Minimization
- Molecular dynamics.
Protein structure prediction:
- Secondary structure
- Homology modeling
- Fold racognition
- ab-initio

Lessons

1	24.2.03	Introduction Experimental structure determination pdf ppt
2	10.3.05	Sequence alignment ppt pdf homologous proteins sequence alignment substitution matrices and scores global alignment algorithm Section II: amino acid quiz DeepView tutorial 1-6 Homework - due 23.3.05
3	17.3.05	BLAST ppt pdf
4	31.3.05	PSI-BLAST ppt pdf
5	7.4.05	Family searches, profile-profile searches and multiple sequence alignment ppt pdf
6	14.4.05	Why do proteins fold? I ppt pdf Homework due to 1/5/05 tutorial Do not do the homology modeling part. template and comments
7	19.5.05	Why do proteins fold? II, semi-empirical energy functions, minimization I ppt pdf
8	26.5.05	Minimization II, molecular dynamics ppt, pdf
9	1.6.05	Simulated annealing ppt, pdf
10	8.6.05	More energy functions, structure comparison and clasification, homology modeling ppt, pdf
11	16.6.05	Protein structure prediction. ppt, pdf

DeepView (Swiss PDB Viewer) is the major software package we use in the course.
- this is where you get it
- This is the tutorial by Gale Rhodes

Important links

BGU Bioinformatics Support unit
Includes many more links.
The Protein Data Bank (PDB)
NCBI
bioinfo.pl
Structural Classification of Proteins (SCOP)
Some (relatively) good prediction tools by Sander & Rost
Swissprot
The official home page of CASP6
Jpred

Recommended reading

Introduction to Protein Structure Branden & Tooze (Garlend Publishing)
PROTEINS Structure, Function and Genetics supplement 3,1999
BLAST & PSI-BLAST
ClustalW
Tcoffee
MUSCLE

Grading
Final Grade = 40% homework + 5% quiz + 55% final exam.

Acknowledgments

Thanks to Dmitry Voronov for the graphic interface to the 2D simulations
I am grateful to Gale Rhodes , Kevin Cowtan , Itai Yanai , Mark Blaxter and Julia Shifman for making their teaching material publicly available, and allowing me to use it for teaching in this course.