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.

    Last modified: 07/18/2015          Go to Mezei Lab Home page