Data
Official data in SubjectManager for the following academic year: 2023-2024
Course director
-
Dr. Rita Judit BÖRZSEI
assistant professor,
Department of Pharmacology and Pharmacotherapy -
Number of hours/semester
lectures: 0 hours
practices: 12 hours
seminars: 0 hours
total of: 12 hours
Subject data
- Code of subject: OSF-FIG-T
- 1 kredit
- Dentistry
- Optional modul
- spring
-
Course headcount limitations
min. 5 – max. 40
Available as Campus course for 40 fő számára. Campus-karok: ÁOK GYTK
Topic
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.
Lectures
Practices
- 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.
Seminars
Reading material
Obligatory literature
Literature developed by the Department
The educational material will be available on NEPTUN Meet Street in digital form.
Notes
Recommended literature
Alan Hinchliffe: Molecular Modelling for Beginners, Wiley, Chichester, U.K. 2003.
Conditions for acceptance of the semester
Maximum of 25 % absence allowed
Mid-term exams
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
Exam topics/questions
They will be available on Neptun Meet Street in digital form.
Examiners
Instructor / tutor of practices and seminars
- Dr. Börzsei Rita Judit
- Dr. Zsidó Balázs Zoltán