Protein Bioinformatics

<p>1 Proteins</p> <p>1.1 Building blocks</p> <p>1.2 Hierarchical representation of proteins</p> <p>1.3 Structural classification of proteins</p> <p>1.4 Databases for protein sequences</p> <p>1.5 Exercises</p> <p>1.6 References</p> <p>2. Protein Sequence Analysis</p> <p>2.1 Sequence alignment</p> <p>2.2 Programs for aligning protein sequences</p> <p>2.3 Amino acid properties</p> <p>2.4 Amphipathic character of a-helices and b-strands</p> <p>2.5 Online tools for sequence analysis</p> <p>2.6 Exercises</p> <p>2.7 References</p> <p>3 Protein Structure Analysis</p> <p>3.1 Assignment of secondary structures</p> <p>3.2 Computation of solvent accessibility</p> <p>3.3 Representation of solvent accessibility</p> <p>3.4 Residue-residue contacts</p> <p>3.5 Amino acid clusters in protein structures</p> <p>3.6 Contact potentials</p> <p>3.7 Cation--p interactions in protein structures</p> <p>3.8 Non canonical interactions</p> <p>3.9 Free energy calculations</p> <p>3.10 Amino acid properties derived from protein structural data</p> <p>3.11 Parameters for proteins</p> <p>3.12 Exercises</p> <p>3.13 References</p> <p>4. Protein Folding Kinetics</p> <p>4.1 F value analysis</p> <p>4.2 Experimental studies</p> <p>4.3 Relationship between amino acid properties and F values</p> <p>4.4 Hydrophobic clusters and long-range contact network in F value analysis</p> <p>4.5 Kinetic database for proteins</p> <p>4.6 Prediction of protein folding rates</p> <p>4.7 Relationship between F values and folding rates</p> <p>4.8 References</p> <p>5. Protein Structure Prediction</p> <p>5.1 Secondary structure</p> <p>5.2 Protein structural class</p> <p>5.3 Secondary structure content</p> <p>5.4 Discrimination of transmembrane helical proteins and predicting their membrane spanning segments</p> <p>5.5 Discrimination of transmembrane strand proteins</p> <p>5.6 Identification of membrane spanning b -strand segments</p> <p>5.7 Solvent accessibility</p> <p>5.8 Inter-residue contact prediction</p> <p>5.9 Protein tertiary structure prediction</p> <p>5.10 Webservers for protein structure prediction</p> <p>5.11 Exercises</p> <p>5.12 References</p> <p>6 Protein Stability</p> <p>6.1 Determination of protein stability</p> <p>6.2 Thermodynamic database for proteins and mutants</p> <p>6.3 Relative contribution of non-covalent interactions to protein stability</p> <p>6.4 Stability of thermophilic proteins</p> <p>6.5 Analysis and Prediction of protein mutant stability</p> <p>6.6 Exercises</p> <p>6.7 References</p> <p>7 Protein Interactions</p> <p>7.1 Protein-protein interactions</p> <p>7.2 Protein-DNA interactions</p> <p>7.3 Protein-RNA interactions</p> <p>7.4 Protein-ligand interactions</p> <p>7.5 Exercises</p> <p>7.6 References</p> <p>Appendix A List of protein databases/webservers</p>