NCBR002 From Supramolecular Chemistry to Structural Biology by Multiscale Modelling Methods

Faculty of Science
Spring 2024
Extent and Intensity
1/2/0. 4 credit(s). Type of Completion: k (colloquium).
Teacher(s)
RNDr. Petr Kulhánek, Ph.D. (lecturer)
Mgr. Jan Novotný, Ph.D. (lecturer)
Ing. Tomáš Trnka, Ph.D. (lecturer)
doc. Mgr. Karel Kubíček, PhD. (lecturer)
RNDr. Miroslav Krepl, Ph.D. (lecturer)
Mgr. Július Zemaník (lecturer)
prof. RNDr. Robert Vácha, PhD. (lecturer)
Mgr. Filip Melicher (lecturer)
Denys Biriukov, Ph.D. (lecturer)
William Shakespeare Morton, PhD (lecturer)
Mgr. Ivo Kabelka, Ph.D. (lecturer)
Guaranteed by
RNDr. Petr Kulhánek, Ph.D.
National Centre for Biomolecular Research – Faculty of Science
Supplier department: National Centre for Biomolecular Research – Faculty of Science
Prerequisites
SOUHLAS
This course is intended for students registered in the Intensive Summer School program (https://summeratmasaryk.cz/). We also accept a few highly motivated students from Masaryk University upon mutual agreement.
Course Enrolment Limitations
The course is offered to students of any study field.
Course objectives
Computer simulations have become a valuable tool for expanding our knowledge in many areas. The steadily increasing performance of supercomputers allows us to simulate bigger systems more accurately. However, proper predictions can only be obtained if correct models and theoretical approaches are employed. Therefore, this course aims to provide essential foundations for performing computer simulations and ways to avoid typical errors from misunderstanding employed approximations. The lectures will span various molecular modelling methods addressing problems from supramolecular chemistry to structural biology. The course will comprise theoretical lectures complemented by practical sessions exercising typical simulation techniques in each discipline.
Learning outcomes
The student will gain a broad understanding of molecular modeling techniques. With this knowledge, they will be able to begin basic projects on a range of topics, from supramolecular chemistry to structural biochemistry.
Syllabus
  • 1) Basics from phenomenological and statistical thermodynamics.
  • 2) Physical foundations of interaction within and between atoms.
  • 3) How to build suitable models ranging from small to very large biomolecular systems.
  • 4) Chemistry models include quantum mechanics (QM), molecular mechanics (MM), and their hybrid versions, particularly QM/MM.
  • 5) Sampling techniques for the free energy calculation, employing an ideal gas model and potential of mean force (PMF) methods, including umbrella sampling, adaptive biasing force, and their accelerated versions by a multiple-walker approach.
  • 6) Impact of collective variables on calculated free energies.
  • 7) How to simulate biomolecular systems properly.
  • 8) Impact of pH on ionizable groups and reconstruction of experimentally unresolved protein structure parts.
  • 9) Protein structure prediction by machine learning methods (AlphaFold, ESMFold, RoseTTAFold).
  • 10) Docking to prepare protein/substrate complexes.
  • 11) Simulations employing reactive force field (ReaxFF).
Teaching methods
lectures, class discussions, projects on computers, excursions to CEITEC core laboratories
Assessment methods
solving projects during the course, class discussions, knowledge surveys
Language of instruction
English
Further comments (probably available only in Czech)
The course can also be completed outside the examination period.
The course is taught annually.
The course is taught: in blocks.
Teacher's information
https://www.ncbr.muni.cz/en/for-students/summer-schools/2024/multiscale-modelling-methods
This course lasts two weeks (10 days of classes), with 5 teaching hours daily.

In 2024, the course will be held in computer classroom 118/C04 at University Campus Bohunice every working day from 9:00 to 15:00 from 15th to 26th July.

The course is also listed under the following terms Spring 2023.
  • Enrolment Statistics (recent)
  • Permalink: https://is.muni.cz/course/sci/spring2024/NCBR002