Biomolecules: Databanks, Visualization and Computations


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Homepage to the lecture 'Biomolecules: Databanks, Visualization and Computations'

I recently moved to the University of Minho, Braga, Portugal. Therefore the lecture has been discontinued in Jena. However I will continue to maintain these pages.

To the lecture 'Biophysical Chemistry' and all other lectures

Lecture Winter term 2007/2008 , Mi.,16:00 - 18:00 Multimediazentrum-2, Raum 1225/1227, Ernst-Abbe-Platz_4

Schedule (german, pdf -format)

Schein (in German)

Programs and resources used during the class

VMD scripts, vibrational animations

Homework proposals (in german)

Summary: Biochemistry by Computer

The potential to use computers for visualization of biomolecules and to perform some calculations like molecular dynamics and docking has been significantly improved in the past years. The goal of the lecture with exercises is to give an introduction into the possibilities of some programs, which perform these tasks. The programs are mostly freeware of some kind, which allows participants to use the programs outside the classroom. Links to the used programs and resources are collected on a separate page. In the frame of the class, specific types of proteins like chromoproteins, protein-nucleic acid complexes, antibodies and engineered proteins are particularly featured, but the techniques used are generally applicable for all biomolecules.


Originally this class was part of the lecture "Biophysical Chemistry I and II" by R. Glaser, K.O. Greulich and P. Schellenberg, and some of the proteins taken as examples are also featured in these lectures. Furthermore, this introduction is also very useful for the lecture "Molekulare Strukturbiologie" by M. Görlach and possibly for other classes taught in Jena. However participation is independent of these lectures and everybody is wellcome.

The class is conducted as a 2 to 3 hour lecture / exercise per week. A computer will be available for every student. Typically, an hands-on introduction in the resp. topic is given by the lecturer first, after which the participants can try out the techniques on their own. The operating system used is WinXP, which has the advantage that most users are familiar with this, and the disadvantage that some scientific programs rather run under Unix and will therefore not be available.

The central part will be hand-on program introductions with some guidance, in which everybody can try out the introduced programs, all of which are (sort of) freeware. The focus will be on the visualization of biological macromolecules, based on the protein data bank file format (pdb). The program particularly featured is Visual Molecular Dynamics (VMD) from the University of Illinois at Urbana-Champain and the corresponding molecular dynamics package NAMD. Additionally Chime, Rasmol Pymol and similar programs are shown. Furthermore, there will be an introduction into protein dynamics and protein interaction calculations for example by using the programs NAMD and Hex, respectively.

A short overview on quantum mechanical calculation of small molecules is also included. To this end, the graphical user interface oscail in connection with Mopac6 , Gamess and Tinker is used. The conductance of this part depends on the number of participants and the specific interests.

Around 24 computers are available, and you are encouraged to bring your own labtop to the seminars. Although all of the programs used are free of charge for education and research, some (for example VMD, Molekel) require registrations prior to downloading. These programs will only be installed on private computers after the proper registration. The use of some data storage medium like an USB --stick is strongly advisable! A CD with lecture notes, pdb -files, script -files, computational input and output files, user manuals and those programs available without registration will be distributed solely to participants.

For questions, please contact:
Peter Schellenberg, phone phone (+351) 253-604074

Peter Schellenberg 2008-may-09