MSc yr1-2 spring
After a successful completion of this course, students will have
This course aims at emphasizing the quantitative aspects of scientific research. For this, the course contains three intertwined components: (i) searching and evaluating nucleic acid and protein structural data from various databases, (ii) use of scientific computing to study structural, dynamical, functional and thermodynamical properties of proteins and membranes and their interaction with other molecules, and (iii) using biocomputing tools to access and analyze large and high-throughput data produced and accessible through biochemical and computational experiments.
Students will learn to access biological databases, search and retrieve relevant data, analyze data in a meaningful manner, and link data and results obtained from different tools. A very brief introduction to metabases and data compilation is provided as well. Interaction studies are emphasized through genome-wide mapping of protein-DNA interaction, proteomics-based bioinformatics, and high-throughput mapping of protein-protein interaction networks. Commonly employed modeling and simulation techniques will also be dealt with. These include molecular dynamics, Monte Carlo and Langevin (stochastic, Brownian) dynamics, continuum electrostatics, statistical thermodynamics, protein modeling techniques, protein-ligand docking, protein-ligand affinity calculations and the computer simulation of the protein folding process and enzyme action.
Face to face teaching
74 h contact sessions. Lectures and practicals, student tasks, including the presentation of an original article. Attendance to practicals and article presentation are mandatory.
MSc / Protein science and biotechnology
1. Big data in biomedicine (http://www.nature.com/nature/outlook/big-data/)
2. Holzinger, A. Biomedical informatics, Springer, Heidelberg, 2014. 3. PubMed (Publications) (http://www.ncbi.nlm.nih.gov/pubmed/)
4. Leach, A.R., Molecular modelling. Principles and applications, Second edition, Prentice Hall, New York, 2001
5. Berendsen, H.J.C Simulating the physical world. Hierarchial modeling from quantum mechanics to fluid dynamics., Cambridge University Press, Cambridge, 2007
1. GenBank (DNA) (http://www.ncbi.nlm.nih.gov/nucleotide)
2. Ensembl and Ensembl Genomes (Genome) (http://www.ensembl.org/ and http://ensemblgenomes.org/)
3. UniProt (Protein) (http://www.uniprot.org/)
4. DIP and BioGrid (Protein Interaction) (http://dip.doe-mbi.ucla.edu/dip/Main.cgi and http://thebiogrid.org/)
5. PDB (protein structure database) (http://www.rcsb.org/)
6. Entrez (http://www.ncbi.nlm.nih.gov/gquery/gquery.fcgi)
Practicals evaluation, article presentation, group discussion, and project report. No exam.
Location of instruction: Kontinkangas campus