Molecular Modeling Course Description
The course meets once a week for an hour, but students are expected to
work through the
tutorials
of the various programs involved.
Tha meeting is at a time mutually conveient to the students
to avoid conflict with their (usually more strict) laboratoy schedules.
During the
meeting the concepts behind the computer modeling approaches are
discussed, and the problems encountered using the programs are clarified.
The course relies mainly on academic software (e.g.,
VMD from University of Illinois at Urbana-Champaign,
Simulaid and Dockres developed here) as well as on commercial
software (Gaussian, Pymol and Schrodinger's suit).
An additional component is the use of Web
resources (e.g., the Protein Data Bank or the ZINC library of small
molecules).
The modeling functions that will be acquired through the course include
(but is not limited to) the followings:
Creation of various molecules on the screen
Manipulation of molecules: Color, label, measures of
geometrical parameters, display of surfaces
Energy minimization of structures
Comparison of structures
Creation of biopolymers (polypetides and nucleic acids)
Manipulation and visualization of biopolymers
Calculating electrostatic properties of macromolecules
Running ab-inito or semiempirical quantum chemistry
Docking of molecules
Analysis of simulation results
Using WWW resouldes for molecular modeling
The final grade is given on the basis of a report that the students
submit. The report includes a brief review of the conceptual background
of the methodologies, a description of the system that was studied and a
summary of the simulation and the analysis.
Students will have to have an account on the server Minerva.
This course is based on state-of-the-art approaches and resources and
hence is in a permanent state of development. Student and user feedback
are expected in order to assess the adequacy of the tutorial material and
to be able to recognize and respond to the need for additional sources of
information.
