Pharmacoinformatics in the Practice


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: OPF-FIG-T
  • 1 kredit
  • Pharmacy
  • Optional modul
  • spring


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.


Reading material

Obligatory literature

Literature developed by the Department

The educational material will be available on NEPTUN Meet Street in digital form.


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.


Instructor / tutor of practices and seminars

  • Dr. Börzsei Rita Judit
  • Dr. Zsidó Balázs Zoltán