C9087 Computational Chemistry for Structural Biology

Faculty of Science
Spring 2020
Extent and Intensity
2/0. 2 credit(s) (plus 1 credit for an exam). Recommended Type of Completion: zk (examination). Other types of completion: k (colloquium).
Teacher(s)
prof. RNDr. Jaroslav Koča, DrSc. (lecturer)
Mgr. Stanislav Kozmon, Ph.D. (lecturer)
Mgr. Zdeněk Kříž, Ph.D. (lecturer)
RNDr. Petr Kulhánek, Ph.D. (lecturer)
Mgr. Martin Prokop, Ph.D. (lecturer)
doc. RNDr. Radka Svobodová, Ph.D. (lecturer)
prof. RNDr. Robert Vácha, PhD. (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
basic knowledge of general and physical chemistry
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
there are 6 fields of study the course is directly associated with, display
Course objectives
The computational chemistry is a discipline that uses computers to predict behaviour of (bio)molecular systems. Its advantage resides in good resolution that in many cases overcome experimental data. On the other hand, it usually suffers from smaller precision. The course will provide balanced overview of available methods, used approximations and limits of computer simulations. Using selected examples, students will be taught how the computational chemistry might help them in better understanding of processes studied in their projects.
Learning outcomes
The computational chemistry is a discipline that uses computers to predict behaviour of (bio)molecular systems. Its advantage resides in good resolution that in many cases overcome experimental data. On the other hand, it usually suffers from smaller precision. The course will provide balanced overview of available methods, used approximations and limits of computer simulations. Using selected examples, students will be taught how the computational chemistry might help them in better understanding of processes studied in their projects.
Syllabus
  • 1) Introduction: general concepts in computational chemistry.
  • 2) Potential Energy versus Structure: quantum nature of molecular systems, potential energy versus structure versus function, computer representation of structures, properties of potential energy surface, connection to statistical thermodynamics.
  • 3) Quantum Mechanics: introduction to quantum chemical calculations, methods overview, application of quantum mechanics to quantify essential interactions in biomolecular systems, reaction mechanisms studied by hybrid QM/MM methods.
  • 4) Molecular Mechanics: simplified relationship between structure and energy, description of conformational changes, search for global energy mimima, folding.
  • 4) Docking: principles of molecular docking, scoring methods, searching algorithms, computational docking in drug discovery, virtual screening, protein-protein docking, prediction of oligomeric structures and molecular assemblies.
  • 5) Rational Protein Design: principles of rational protein design by computer modelling, construction of modified proteins by site-directed mutagenesis and homology modelling, assessment of properties of modified proteins by computational methods.
  • 6) Molecular Simulations: molecular dynamics, principles, advantages and disadvantages, how to model solvents and ions, post-simulation analysis.
  • 7) Coarse-grained Simulations: introduction to models and methods of coarse grained simulations.
  • 8) Chemoinformatics: Introduction to chemoinformatics, molecular descriptors, similarity methods, Quantitative Structure-Property Relationship modelling.
Literature
    recommended literature
  • J. Alvarez, B. Shoichet: Virtual Screening in Drug Discovery. 2005. ISBN 978-0824754792
  • J.Gu, P.E.Bourne: Structural bioinformatics. 2009. ISBN 978-0-470-18105-8
  • Bajorath, J.: Chemoinformatics Concepts, Methods, and Tools for Drug Discovery. Humana Press Totowa, New Jersey, 2004.
  • CRAMER, Christopher J. Essentials of computational chemistry : theories and models. 2nd ed. Chichester: John Wiley & Sons, 2004, xx, 596. ISBN 0470091819. info
  • Chemoinformatics :a textbook. Edited by Johann Gasteiger - Thomas Engel. Weinheim: Wiley-VCH, 2003, xxx, 649 s. ISBN 3-527-30681-1. info
  • LEACH, Andrew R. Molecular modelling : principles and applications. 2nd ed. Harlow: Prentice Hall, 2001, xxiii, 744. ISBN 0582382106. info
Teaching methods
lectures, class discussion
Assessment methods
written test followed by oral exam
Language of instruction
English
Follow-Up Courses
Further Comments
Study Materials
The course is taught annually.
The course is taught: in blocks.
The course is also listed under the following terms spring 2012 - acreditation, Spring 2013, Spring 2014, Spring 2015, Spring 2017, spring 2018, Spring 2019, Spring 2021, Spring 2022, Spring 2023, Spring 2024, Spring 2025.
  • Enrolment Statistics (Spring 2020, recent)
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