Molecular Modeling

1. Regarding computer laborations

Welcome! This course is focused on learning theoretical and computational techniques to predict, model, and simulate structure of biological macromolecules. More information will be added here before the course; the first lecture will be abbreviated and given back-to-back with the first lecture of the structural biochemistry course to facilitate synchronization for students who would like to take both courses.

The book used in this course is:

Molecular Modelling, Principles and Applications

Andrew R. Leach

Pearson Eduction, ISBN: 978-0-582-38210-7

Questions? You can reach Berk Hess directly at hess[at]cbr.su.se

Tentitative schedule fall 2010

Monday November 1, 15:15-17:00 (red room)
Lecture 1: introduction, protein structure and interactions
Wednesday November 3, 15:15-17:00 (red room)
Lecture 2: Analysis of proteins, structure, interactions, and stabilization
Friday November 5, 13:15-15:00 (red room)
Lecture 3: Force fields describing interactions in biomolecules
Monday November 8, 15:15-17:00 (red room)
Lecture 4: Energy landscapes and minimization methods
Tuesday November 9, 15:15-17:00 (red room)
Lecture 5: Computer Simulation techniques
Thursday November 11, 15:15-17:00 (red room)
Lecture 7: Fold recognition from sequence
Monday November 15, 15:15-17:00 (red room)
Lecture 6: More about minimization & simulation. Repetition, Q & A session.
Wednesday November 17, 13:15-17:00 (computer room)
Lab 1: Molecular graphics

Thursday November 18, 13:15-15:00 (red room)
Lecture 7: Fold recognition from sequence
Friday November 19, 13:15-17:00 (computer room)

Lab 2: Molecular simulation
Monday November 22, 15:15-17:00 (red room)
Lecture 8: Comparative modeling of protein structure
Wednesday November 24, 13:15-17:00 (computer room)

Lab 3: Comparative modeling of proteins
Friday November 26, 15:15-17:00 (red room)
Lecture 9: The CASP experiment and prediction metaservers
Wednesday December 1, 13:15-15:00 (red room)
Lecture 10: Free energy calculation through simulation
Friday December 3, 13:15-15:00 (red room)

Lecture 12: Drug design, chemoinformatics and pharmacoinformatics
Thursday December 9, 13:00-17:00 (computer room)
Lab 4: Docking
Monday December 13, 13:15-15:00 (red room)
Lecture 11: Using ROSETTA for protein structure prediction
Tuesday December 14, 11:15-12:00 (red room)
Lecture 13: Q & A session before exam
.
Friday December 17, 9:00-14:00 (computer room)
Written exam

Regarding computer laborations

(i) Log out: When you are leaving the computer lab for the day, please log out from your computer! This means that the screen will not be locked when someone else comes along and wants to use the machine.
(ii) Size of report: Although high-resolution pictures are nice, please convert them so that the size of the report is < 5 MB. Also, we love pdf:s...
(iii) Deadline for lab reports: All lab reports should be sent by e-mail (to Christine Sophie Schwaiger - cschwaig@cbr.su.se) before the next lab. The last lab report is due on Dec 18.
(iv) Status of lab reports: The status of the lab reports can be found here.
(v) Passing the lab course: All lab reports that is not labelled as PASSED before January 15 will need to be done again the next time the course is given.