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Educational and
professional goals:
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Learning practical skills in basic bioinformatics: specific tools, Internet services, programming of simple practical tasks and computer visualization of the results.
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Course description:
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The way the information is stored in DNA and protein sequences. Genome sequencing. Relations between sequences, structures and functions of biopolymers. The role of bioinformatics in biology, medicine, pharmacology and biotechnology. Comparisons of DNA and protein sequences. Protein sequence databases (GenBank, SwissProt, PDB). Format of databases’ sequences. Substitution matrices. Sequence profiles and their role. Sequence alignment. Programs Blast, PsiBlast and Fasta. Multiple sequence alignments. Databases PROSITE, Pfam, BLOCKS. Programs CLUSTAL, MSA and MultiAlign. Three dimensional protein structures. Structural database PDB. PDB formats. Visualization of protein structures. Programs RasMol and Biodesigner. Analysis of protein structures. Comparisons of protein structures. Structural alignment. Root-mean-square deviation between structures. Secondary structure prediction. DSSP classification of secondary structures. Other definitions of secondary structure. Programs PHD and PsiPRED. Protein threading. Sequence-structure alignments in protein structure prediction. Various levels of threading. Threading servers. Metaservers. Prediction of protein structures and function. Comparative modeling, threading and ab initio methods. Programs Swiss-Model and MODELLER. Ligand docking.
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