1. Day What is bioinformatics, top 10 challenges in bioinformatics, Tree of life, from DNA to cell function, overview: biological information and methods of bioinformatics, history of bioinformatics Databases, NCBI, Entrez, Genebank 2. Day Aminoacid and their properties, Why sequence comparison, Pairwise sequence alignments, Dayhoffs accepted point mutations, PAM matrices, BLOSUM Matrices, Calculation of alignment score, Dot-plots, Dynamic programming according to Needleman-Wunsch, local alignments according to Smith Waterman, heurestic methods FASTA and BLAST. 3. Day BLAST, word size, expect value, threshold Multiple alignments, Protein domains and motifs, Protein Data Bank, Types of protein representation 4. Day Phylogenetic trees, background, Molecular clock hypothesis, Rate of nucleotide substition, time of divergence, tree-building methods, Bootstrapping 5. Day Protein structure prediction, protein secondary structure, Secondary structure prediction, Chou-Fassman, Secondary structure and backbone conformation, Tertiary protein structure and folds, structural alignments, Root mean square deviation, temperature factor, Protein structure modeling, Levinthal paradox, energy landscapes, Force field theory, Homology modeling, general aspects, fragment based, restraint based approaches, loop modeling, spatial contraints, Verification of folds. 6. Day Molecular dynamics, verlet algorithm, lipid membranes, boundary condition Modeller homology modelling, building of a simple model, refinement of loop regions, model accuracy 7. Day Yasara moleular dynamics, building of a salt bridge, building of a disulfide bridge, accurate simulation of a protein in aqueos solution 8. Day Autodock- docking flexible-static, genetic algorithms, Monte-Carlo simulated annealing
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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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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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