| Proteins | |
| Building blocks | |
| Hierarchical representation of proteins | |
| Structural classification of proteins | |
| Databases for protein sequences | |
| Exercises | |
| References | |
| Protein Sequence Analysis | |
| Sequence alignment | |
| Programs for aligning protein sequences | |
| Amino acid properties | |
| Amphipathic character of a-helices and b-strands | |
| Online tools for sequence analysis | |
| Exercises | |
| References | |
| Protein Structure Analysis | |
| Assignment of secondary structures | |
| Computation of solvent accessibility | |
| Representation of solvent accessibility | |
| Residue-residue contacts | |
| Amino acid clusters in protein structures | |
| Contact potentials | |
| Cation--p interactions in protein structures | |
| Non canonical interactions | |
| Free energy calculations | |
| Amino acid properties derived from protein structural data | |
| Parameters for proteins | |
| Exercises | |
| References | |
| Protein Folding Kinetics | |
| F value analysis | |
| Experimental studies | |
| Relationship between amino acid properties and F values | |
| Hydrophobic clusters and long-range contact network in F value analysis | |
| Kinetic database for proteins | |
| Prediction of protein folding rates | |
| Relationship between F values and folding rates | |
| References | |
| Protein Structure Prediction | |
| Secondary structure | |
| Protein structural class | |
| Secondary structure content | |
| Discrimination of transmembrane helical proteins and predicting their membrane spanning segments | |
| Discrimination of transmembrane strand proteins | |
| Identification of membrane spanning b -strand segments | |
| Solvent accessibility | |
| Inter-residue contact prediction | |
| Protein tertiary structure prediction | |
| Webservers for protein structure prediction | |
| Exercises | |
| References | |
| Protein Stability | |
| Determination of protein stability | |
| Thermodynamic database for proteins and mutants | |
| Relative contribution of non-covalent interactions to protein stability | |
| Stability of thermophilic proteins | |
| Analysis and Prediction of protein mutant stability | |
| Exercises | |
| References | |
| Protein Interactions | |
| Protein-protein interactions | |
| Protein-DNA interactions | |
| Protein-RNA interactions | |
| Protein-ligand interactions | |
| Exercises | |
| References | |
| List of protein databases/webservers | |
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