Topics in Bioinformatics and Computational Biology

1. Introduction to biological significance of bioinformatics topics    References     Details    Seminar 1

2. DNA sequence analysis     References    Details    

    2.1. Gene finding

    2.2. non-coding sequences

    2.3. regulatory sequences finding and analysis    References    Details    Seminar 2

    2.4. orthologous and paralogous sequences

    2.5. evolution

3. Protein sequence analysis    References     Details     Seminar 3

    3.1. Measures of similarity in amino acid sequences    References    Details    Seminar 3

    3.1. Alignments    References     Details     Seminar 3

    3.2. Motifs    References    Details    Seminar 3

    3.3. Classification of protein sequences in families    References    Details    Seminar 3

4. Predicting functional structures (DNA - RNA - proteins - lipids - carbohydrates)     References     Details     Seminar 4

    4.1. Measures of similarity in protein structures

    4.1. Homology modeling in proteins

    4.2. ab initio

    4.3. Threading

    4.4. partial information

        - overall architecture

        - binding pocket

        - protein backbone

5. From linear sequence to three-dimensional shapes: protein folding

    5.1. unfolded chain and conformational space

    5.2. folding intermediates

    5.3. driving forces of folding

    5.4. models for protein folding

    5.5. discriminating structures

    5.6. misfolding

    5.7. unfolding

    5.8. conformational ambiguity

    5.9. helpers of folding (chaperones)

6. Molecular interactions

    6.1. Protein-ligand

    6.2. Protein-protein

    6.3. Protein-DNA

    6.4. Protein-RNA

    6.5. Protein-lipid

    6.6. Protein-carbohydrate

7. Metabolic and regulatory networks

8. General challenges and applications:

    8.1. Linking variety of databases

    8.2. Linking the different layers

    8.3. Interpretation of experimental data

    8.4. Design of new experiments

    8.5. Drug screening

    8.6. Genetic variability in individuals and in different strains (host and pathogen)

9. Specific protein families

    9.1. G-protein coupled receptors