C9087 Computational Chemistry for Structural Biology

Přírodovědecká fakulta
jaro 2023
Rozsah
2/0/0. 2 kr. (plus 1 za zk). Doporučované ukončení: zk. Jiná možná ukončení: k.
Vyučující
Mgr. Stanislav Kozmon, Ph.D. (přednášející)
Mgr. Zdeněk Kříž, Ph.D. (přednášející)
RNDr. Petr Kulhánek, Ph.D. (přednášející)
doc. RNDr. Radka Svobodová, Ph.D. (přednášející)
prof. RNDr. Robert Vácha, PhD. (přednášející)
Garance
RNDr. Petr Kulhánek, Ph.D.
Národní centrum pro výzkum biomolekul – Přírodovědecká fakulta
Dodavatelské pracoviště: Národní centrum pro výzkum biomolekul – Přírodovědecká fakulta
Rozvrh
Po 12:00–13:50 C04/118
Předpoklady
basic knowledge of general and physical chemistry
Omezení zápisu do předmětu
Předmět je nabízen i studentům mimo mateřské obory.
Mateřské obory/plány
předmět má 6 mateřských oborů, zobrazit
Cíle předmětu
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.
Výstupy z učení
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.
Osnova
  • 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) Cheminformatics: Introduction to chemoinformatics, molecular descriptors, similarity methods, Quantitative Structure-Property Relationship modelling.
Literatura
    doporučená literatura
  • Bajorath, J.: Chemoinformatics Concepts, Methods, and Tools for Drug Discovery. Humana Press Totowa, New Jersey, 2004.
  • J.Gu, P.E.Bourne: Structural bioinformatics. 2009. ISBN 978-0-470-18105-8
  • J. Alvarez, B. Shoichet: Virtual Screening in Drug Discovery. 2005. ISBN 978-0824754792
  • 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
Výukové metody
lectures, class discussion
Metody hodnocení
written test followed by oral exam
Vyučovací jazyk
Angličtina
Navazující předměty
Informace učitele
The lecture will not be provided in 2023 due to low attendance.
Další komentáře
Předmět je vyučován každoročně.
Předmět je zařazen také v obdobích jaro 2012 - akreditace, jaro 2013, jaro 2014, jaro 2015, jaro 2017, jaro 2018, jaro 2019, jaro 2020, jaro 2021, jaro 2022, jaro 2024, jaro 2025.