Official data in SubjectManager for the following academic year: 2022-2023
Dr. Rita Judit BÖRZSEI
Department of Pharmacology and Pharmacotherapy
Number of hours/semester
lectures: 0 hours
practices: 12 hours
seminars: 0 hours
total of: 12 hours
- Code of subject: OXFFIG-z-T
- 1 kredit
- Optional modul
Course headcount limitations
min. 5 – max. 40
Available as Campus course for 40 fő számára. Campus-karok: ÁOK GYTK
The Pharmacoinformatics in practice course offers the students an insight into the theoretical and practical aspects of computational molecular modelling. This knowledge is suitable to have an overview on a rapidly developing scientific area. The students will get familiar with such programes and file format that are both used by industrial drug development and scientific researchers today. Homology modelling is sufficient to produce the atomic resolution structures of protein drug targets found in the human body. To attach the drug to its experimentally available (or homology modelled) structure, computational docking is widely used. The investigation of this binding mechanism is important for molecular pharmacological researches.
- 1. Introduction into molecular modeling. Learning about PDB file format.
- 2. PyMol grafical interface. Molecule's representation in 3D.
- 3. Molecule's building based on their Lewis-formula and/or sequence.
- 4. RCSB PDB Databank. 3D atomic structure of receptors and enzymes.
- 5. Structural analysis of target-ligand complex.
- 6. Determination of interacting target residues and the type of interaction in a target-ligand complex.
- 7. Theoretical basis of homology modelling
- 8. Homology model building: UniProt Database, BLAST search, Modeller program package.
- 9. Validation of the homology model: Procheck, Ramachandran plot.
- 10. Theoretical basis of docking calculations.
- 11. Docking using on online server.
- 12. Analysis of docking calculation, determination of the optimal binding pose of the ligand.
Literature developed by the Department
The educational material will be available on NEPTUN Meet Street in digital form.
Alan Hinchliffe: Molecular Modelling for Beginners, Wiley, Chichester, U.K. 2003.
Conditions for acceptance of the semester
Maximum of 25 % absence allowed
Students write a multiple-choice test at the end of the course. The result of the test should reach or exceed 60% to be assessable. If the student does not reach 60% performance, he/she will be given two remediation opportinities.
Making up for missed classes
Replacement is possible according to personal consultation
They will be available on Neptun Meet Street in digital form.
Instructor / tutor of practices and seminars
- Dr. Börzsei Rita Judit
- Dr. Zsidó Balázs Zoltán