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Lecturer(s)
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Koutská Anna, Mgr.
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Havlíčková Petra, RNDr.
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Kutá Smatanová Ivana, prof. Mgr. Ph.D.
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Kaščáková Barbora, Mgr. Ph.D.
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Franta Zdeněk, RNDr. Ph.D.
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Course content
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1. Bioinformatics basics: brief history of bioinformatics, molecular sequences and structures (NCBI, UniProt, PDB Data Bank) 2. Sequence alignment: its types (dot plots, dynamic programming according to Needleman-Wunsch, local alignment according to Smith Waterman and online alignment programs), BLAST alignment program, sequence analysis (FASTA) and display of secondary structural elements 3. Primer design and quality control 4. Phylogenetic trees: methods of phylogenetic tree construction and interpretation. 5. Protein structure prediction: protein secondary structure and its prediction, protein tertiary structure (protein folding and sequence homology) 6. Protein structure prediction and modelling using Phyre2 and AlphaFold (AI) online servers 7. Molecular docking: ligand docking and macromolecule docking (HadDock) 8. Molecular dynamics in Yasara/Modeller/Chimera: construction of simple model, construction of salt bridges, construction of disulfide bridges, modification of loop regions, simulation of protein in aqueous solution, determination of model accuracy.
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Learning activities and teaching methods
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Monologic (reading, lecture, briefing), Dialogic (discussion, interview, brainstorming), E-learning, Work with multi-media resources (texts, internet, IT technologies), Individual tutoring
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Learning outcomes
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The subject Bioinformatics - a field at the interface of biology and computer science - is devoted to the principles of bioinformatics for working with biological sequences and structures of macromolecules. The aim of the course is to acquire basic information about mapping DNA segments, designing PCR primers, searching for known sequences or structural motifs in a protein molecule, and biological databases, their structure and usability. It focuses on the study of computer science methods that can be used to analyze biological databases, including DNA sequences, and concepts of genomics and proteomics. The student will gain hands-on experience with GenBank, EMBL, BLAST, CLUSTAL, for example, used to analyze biological sequences.
Basic orientation in bioinformatics. Mastery of database orientation, modelling methods, molecular dynamics, protein structure prediction.
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Prerequisites
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Basic orientation in biochemistry and molecular biology.
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Assessment methods and criteria
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Combined exam
Active participation and successfully answering at least 50% of the questions on the exam.
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Recommended literature
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A.D. Baxevanis, B.F. Fr. Ouellette. Bioinformatics: A practical Guide to the Analysis of Genes and Proteins, 3rd edition. John Wiley and Sons, NY, TORONTO, 2004.
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Arthur M. Lesk. Introduction to Bioinformatics. Oxford University press, 2002.
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Fatima Cvrčková. Úvod do praktické bioinformatiky. Academia, Praha, 2006. ISBN 80-200-1360-1.
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Chandra Sekhar Mukhopadhyay, Ratan Kumar Choudhary, Mir Asif Iquebal. Basic Applied Bioinformatics. Wiley-Blackwell, 2017. ISBN 978-1-119-24433-2.
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R. Durbin, S. R. Eddy, A. Krogh, G. Mitchison. Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids. Cambridge University Press, Cambridge, UK, 1998.
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