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Multiscale Modelling Methods
From Supramolecular Chemistry to Structural Biology
Computer simulations have become a valuable tool for expanding our knowledge in many areas. The steadily increasing performance of supercomputers or even desktop computers 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.
Program
Classes take place Monday-Friday, 9:00-15:00, with theoretical lectures followed by practical components.
Topics included:
- Basics from phenomenological and statistical thermodynamics.
- Physical foundations of interaction within and between atoms.
- How to build suitable models ranging from small to very large biomolecular systems.
- Chemistry models include quantum mechanics (QM), molecular mechanics (MM), and their hybrid versions, particularly QM/MM.
- 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.
- Impact of collective variables on calculated free energies.
- How to simulate biomolecular systems properly.
- Impact of pH on ionizable groups and reconstruction of experimentally unresolved protein structure parts.
- Protein structure prediction by machine learning methods (AlphaFold, ESMFold, RoseTTAFold).
- Docking to prepare protein/substrate complexes.
- Simulations employing ReaxFF reactive force field.
Students registered in the Intensive Summer School program: The site visits and learning outside the classroom occur in the afternoons. Culture/social activities will take place in the afternoons/nights.
Speakers
The program was delivered by scientists from the six research groups of the National Centre for Biomolecular Research and members of core laboratories from the CEITEC - Central European Institute of Technology. We also had talks given by a researcher of the Institute of Biophysics at The Czech Academy of Sciences and by our graduate who is currently working at CNR - Istituto Officina dei Materiali (IOM) in Trieste, Italy.
Petr Kulhánek * Tomáš Trnka * Július Zemaník * Jan Novotný * Radovan Fiala * Tomáš Klumpler * Filip Melicher * Karel Kubíček * Karel Škubník * Robert Vácha * Denys Biriukov * William Shakespeare Morton * Ivo Kabelka * Miroslav Krepl * Pavel Janoš
Laboratoř výpočetní chemie
Vedoucí: RNDr. Petr Kulhánek, Ph.D.
Peptidová terapeutika
Vedoucí: prof. RNDr. Robert Vácha, PhD.
Struktura biosystémů a molekulárních materiálů
Vedoucí: prof. RNDr. Radek Marek, Ph.D.
Struktura a dynamika nukleových kyselin
Vedoucí: prof. RNDr. Jiří Šponer, DrSc.
Glykobiochemie
Vedoucí: prof. RNDr. Michaela Wimmerová, Ph.D.
Strukturní biologie genové regulace
Vedoucí: prof. Mgr. Richard Štefl, Ph.D.
We visited three core laboratories from CEITEC (NMR, X-Ray diffraction, and CryoEM):
Poster Session
As an option, interested students can bring posters and discuss their research results during the poster session. The preferred poster size is an A3 portrait, which can be printed on-site.
We had one poster:
- Predicting binding events in very flexible, allosteric, multi-domain proteins. By Andrea Basciu, Mohd Athar, Han Kurt, Christine Neville, Giuliano Malloci, Fabrizio C. Muredda, Andrea Bosin, Paolo Ruggerone, Alexandre M. J. J. Bonvin, and Attilio V. Vargiu; Physics Department, University of Cagliari, Cittadella Universitaria, I-09042 Monserrato (CA), Italy
Computational Resources
Since Linux is a mainstream operating system on computational clusters and supercomputers employed for molecular modelling, we will provide students with all the necessary information on working in this environment. We will cover essential work in graphical and command-line Linux environments employing local and remote sessions. Thus, no prior knowledge of working in Linux is necessary (but it will be a plus).
Students can bring their computers (laptops or tables). We will show how to access Linux computers remotely by various techniques (ssh, putty, WinSCP, [no]VNC) from MS Windows, macOS, Linux, and Android OSes.
In addition, students will get access to the national MetaCentrum supercomputing centre. The access will be granted for three months, allowing students to use the knowledge they obtain during summer on their projects.
Acknowledgements
Computational resources were provided by the e-INFRA CZ project (ID:90254), supported by the Ministry of Education, Youth and Sports of the Czech Republic.