C8855 Advanced Molecular Modelling Methods

Faculty of Science
Spring 2025
Extent and Intensity
1/0/0. 1 credit(s) (plus extra credits for completion). Recommended Type of Completion: k (colloquium). Other types of completion: zk (examination).
In-person direct teaching
Teacher(s)
RNDr. Petr Kulhánek, Ph.D. (lecturer)
Guaranteed by
RNDr. Petr Kulhánek, Ph.D.
National Centre for Biomolecular Research – Faculty of Science
Contact Person: RNDr. Petr Kulhánek, Ph.D.
Supplier department: National Centre for Biomolecular Research – Faculty of Science
Prerequisites
Basic level of general and physical chemistry. A basic knowledge of quantum chemistry is an advantage. It is strongly suggested that the student go first through the courses C7790 Introduction to Molecular Modelling or C9087 Computational Chemistry for Structural Biology.
Course Enrolment Limitations
The course is also offered to the students of the fields other than those the course is directly associated with.
fields of study / plans the course is directly associated with
Course objectives
The course is aimed at acquiring advanced knowledge in the field of computational chemistry. Its orientation is strongly application-oriented. The course will discuss the methods needed to build models for simulations of predominantly biomolecular systems. Basic problems of incomplete experimental structures and the appropriateness of using artificial intelligence tools to predict structures will be discussed. The preparation of pre-reaction complexes for studying enzymatic reactions and basic methods for studying reaction mechanisms will also be discussed.
Learning outcomes
The student will gain advanced knowledge to study the dynamics and reactivity of biomolecular systems using molecular modelling tools.
Syllabus
  • Basic requirements for models of biomolecular systems * Limitation of experimental (X-ray, NMR, CryoEM) and predicted (AlphaFold2, ESM-Fold, RoseTTAFold2) structures * Ionizable groups and the effect of pH on the model * Docking of substrates into the active site * How to solvate biomolecular systems correctly * Types of water and ion models * Molecular dynamics (MD) of biomolecular systems * Analysis of MD trajectories * Hybrid QM/MM description of the active site of an enzymatic reaction * Calculation of reaction profiles * Study of reaction mechanisms
Literature
  • Encyclopedia of computational chemistry. Edited by Paul von R. Schleyer. Chichester: John Wiley & sons, 1998, xxix, 812. ISBN 047196588X. info
  • LEACH, Andrew R. Molecular modelling : principles and applications. 2nd ed. Harlow: Prentice Hall, 2001, xxiii, 744. ISBN 0582382106. info
  • JENSEN, Frank. Introduction to computational chemistry. Third edition. Chichester: Wiley, 2017, xxii, 638. ISBN 9781118825990. info
Teaching methods
Lectures combined with discussions.
Assessment methods
The course ends with a written test followed by an optional oral examination.
Language of instruction
Czech
Further Comments
The course can also be completed outside the examination period.
The course is taught annually.
The course is taught: every week.
The course is also listed under the following terms Spring 2008 - for the purpose of the accreditation, Spring 2011 - only for the accreditation, Spring 2002, Spring 2003, Spring 2004, Spring 2005, Spring 2006, Spring 2007, Spring 2008, Spring 2009, Spring 2010, Spring 2011, Spring 2012, spring 2012 - acreditation, Spring 2013, Spring 2014, Spring 2015, Spring 2016, Spring 2017, spring 2018, Spring 2019, Spring 2020, Spring 2021, Spring 2022, Spring 2023, Spring 2024.
  • Enrolment Statistics (recent)
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