Computational Molecular Engineering


Official data in SubjectManager for the following academic year: 2023-2024

Course director

  • Dr. Csaba HETÉNYI

    associate professor,
    Department of Pharmacology and Pharmacotherapy

Number of hours/semester

lectures: 12 hours

practices: 0 hours

seminars: 0 hours

total of: 12 hours

Subject data

  • Code of subject: OTF-CME-T
  • 1 kredit
  • Biotechnology BSc
  • Optional modul
  • spring


Course headcount limitations

min. 5 – max. 25

Available as Campus course for 5 fő számára. Campus-karok: ÁOK ETK GYTK TTK


Computational molecular engineering is a central, modern field of drug design. Theoretical and practical introduction is provided with details of relevant softwares. In Journal Club sessions, recent research articles will be featured with the students to deepen their knowledge in the areas discussed during the previous lectures. In this way, the students can discover further connections themselves and make sure of the usefulness of their newly obtained knowledge in molecular engineering. The lectures will take place weekly or (if possible) contracted into 4 blocks.


  • 1. Visualization of macromolecules. Programs VMD and PyMol - Dr. Hetényi Csaba
  • 2. Structural measurements, editing and comparisons - Dr. Hetényi Csaba
  • 3. An introduction to macromolecular structures. Main features of peptide and protein structures. Experimental sources of structural data of biopolymers - Dr. Hetényi Csaba
  • 4. Examples on structural variability. The role of conformational disorders of proteins in the pathomechanism of Alzheimer’s and prion diseases. Myosin, the motor protein: same sequence with different structures - Dr. Hetényi Csaba
  • 5. Surface and volume calculations - Dr. Hetényi Csaba
  • 6. Simple methods for binding site detection and cavity search. Program PASS - Dr. Hetényi Csaba
  • 7. Hierarchy of calculation methods. Fundamentals of QM - Dr. Hetényi Csaba
  • 8. Programs for molecular modeling - Dr. Hetényi Csaba
  • 9.  Principles of molecular mechanics (MM). Force fields. Bonding and non-bonding interactions - Dr. Hetényi Csaba
  • 10. The general algorithm of MM programs. Program packages. TINKER - Dr. Hetényi Csaba
  • 11. Journal club 1. Computational methods and strategies of drug design - Dr. Hetényi Csaba
  • 12. Journal club 2. Complementary approaches - Dr. Hetényi Csaba



Reading material

Obligatory literature

Literature developed by the Department

The material of the course including pdfs of lectures and lists of questions will be made downloadable from the web site of the Department of Pharmacology and Pharmacotherapy or a link will be provided during the lectures / in an e-mail.


Recommended literature

Conditions for acceptance of the semester

Maximum of 25 % absence allowed

Mid-term exams

There is a final test announced at the end of the semester. The test will include multiple choice questions or short essays. A mark is offered according to the results of the written test or optionally by evaluation of the student's presentation prepared for the Journal Club. The student can improve the mark according to university regulations.

Making up for missed classes

Replacement is possible according to personal consultation.

Exam topics/questions

Lists of questions will be provided at the end of each lecture specifying the required knowledge.


Instructor / tutor of practices and seminars