C2137 Advanced chemoinformatics - seminar

Faculty of Science
Autumn 2023
Extent and Intensity
0/1/0. 1 credit(s) (plus extra credits for completion). Type of Completion: z (credit).
Teacher(s)
doc. RNDr. Karel Berka, Ph.D. (lecturer)
doc. RNDr. Radka Svobodová, Ph.D. (lecturer)
Guaranteed by
doc. RNDr. Radka Svobodová, Ph.D.
National Centre for Biomolecular Research – Faculty of Science
Supplier department: National Centre for Biomolecular Research – Faculty of Science
Prerequisites
NOW ( C2136 Advanced chemoinformatics )
Course Enrolment Limitations
The course is offered to students of any study field.
Course objectives
QSPR modelování: Návrh QSPR modelu avpro predikci pKa. Konkrétní kroky: Výběr deskriptorů, ověření vhodnosti výběru deskriptorů, parametrizace modelu, testování a validace modelu, cross-validace modelu, úpravy a zpřesňování modelu. Práce s různými nástroji pro tvorbu QSPR modelů (Ochem, ChemBench, QSPR Designer, atd.). Vyhledávání dat v chemoinformatických databázích: Vyhledávání molekul z vybraných chemických skupin a vytváření vlastní chemoinformatické datové sady, vyhledávání vlastností a výpočet deskriptorů pro dané molekuly, aplikace získaných datových sad pro tvorbu QSPR modelů. Virtuální screening: Metoda molekulového dokování, skórovací funkce, práce s programem AutoDock.
Learning outcomes
After finishing of the seminar, a student will be able to perform key chemoinformatics analyses and utilise chemoinformatics software tools in praxis.
Syllabus
  • QSPR modeling: Design of QSPR model for pKa prediction. Particular steps: Selection of descriptors, check of descriptor relevance, parameterization of themodel, testing and validation of the model, cross-validation of the model, adjusting and improving of the model. Work with different tools for QSPR model design and implementation (Ochem, ChemBench, QSPR Designer, atd.).
    Searching for data in chemoinformatics databases: Searching for molecules from selected chemical groups and preparation of own data set, searching properties and calculation of descriptors for selected molecules, application of obtained data sets for preparstion of QSPR models.
    Virtual screening: Molecular docking, score function, work with AutoDock software.
Literature
  • • Chemoinformatics Approaches to Virtual Screening. Edited by Alexandre Varnek and Alex Tropsha. Royal Society of Chemistry, 2008
  • • Chemoinformatics Concepts, Methods, and Tools for Drug Discovery. Edited by Jürgen Bajorath. Humana Press Totowa, New Jersey, 2004
  • Handbook of chemoinformatics :from data to knowledge in 4 volumes. Edited by Johann Gasteiger. Weinheim: Wiley-VCH, 2003, xlvii s.,. ISBN 3-527-30680-3. info
  • Chemoinformatics : a textbook. Edited by Johann Gasteiger - Thomas Engel. Weinheim: Wiley-VCH, 2003, xxx, 649. ISBN 9783527306817. info
Teaching methods
solving of examples, performing of analyses
Assessment methods
written test
Language of instruction
Czech
Further Comments
The course can also be completed outside the examination period.
The course is taught once in two years.
The course is taught: in blocks.
The course is also listed under the following terms Spring 2008 - for the purpose of the accreditation, Autumn 2011 - acreditation, Autumn 2013, Spring 2014, Autumn 2014, Autumn 2016, Autumn 2018, Autumn 2020, autumn 2021, Autumn 2024.
  • Enrolment Statistics (Autumn 2023, recent)
  • Permalink: https://is.muni.cz/course/sci/autumn2023/C2137