Protein bioinformatics : from sequence to function / M. Michael Gromiha. — Amsterdam ;Boston : Academic Press / Elsevier, c2010. – (58.17421/G875)

Contents

    Contents
    
    Foreword
    Preface
    Acknowledgments
    1 Proteins
    1.1 Building blocks
    1.2 Hierarchical representation of proteins
    1.3 Structural classification of proteins
    1.4 Databases for protein sequences
    1.5 Protein structure databases
    1.6 Literature databases
    1.7 Exercises
    References
    2 Protein Sequence Analysis
    2.1 Sequence alignment
    2.2 Programs for aligning sequences
    2.3 Amino acid properties
    2.4 Amphipathic character of q-helices and [3-strands
    2.5 Amino acid properties for sequence analysis
    2.6 Exercises
    References
    3 Protein Structure Analysis
    3.1 Assignment of secondary structures
    3.2 Computation of solvent accessibility
    3.3 Representation of solvent accessibility
    3.4 Residue-residue contacts
    3.5 Amino acid clusters in protein structures
    3.6 Contact potentials
    3.7 Cation-q; interactions in protein structures
    3.8 Noncanonical interactions
    3.9 Free energy calculations
    3.10 Amino acid properties derived from protein structural data
    3.11 Parameters for proteins
    3.12 Protein structure comparison
    3.13 Exercises
    References
    4 Protein Folding Kinetics 107
    4.1 Φ-value analysis 107
    4.2 Folding nuclei and Φ-values 115
    4.3 Relationship between amino acid properties and Φ-values 118
    4.4 Φ-value analysis with hydrophobic clusters and long-range contact networks
    4.5 Kinetic database for proteins
    4.6 Prediction of protein folding rates
    4.7 Relationship between oh-values and folding rates
    4.8 Exercises
    References
    5 Protein Structure Prediction 143
    5.1 Protein structural class 143
    5.2 Secondary structure content
    5.3 Secondary structural regions
    5.4 Discrimination of transmembrane helical proteins and predicting their membrane-spanning segments
    5.5 Discrimination of transmembrane strand proteins
    5.6 Identification of membrane-spanning [3-strand segments
    5.7 Discrimination of disordered proteins and domains
    5.8 Solvent accessibility
    5.9 Inter-residue contact prediction .
    5.10 Protein tertiary structure prediction
    5.11 Exercises
    References
    6 Protein Stability
    6.1 Determination of protein stability
    6.2 Thermodynamic database for proteins and mutants
    6.3 Relative contribution of noncovalent interactions to protein stability 218
    6.4 Stability of thermophilic proteins 220
    6.5 Analysis and prediction of protein mutant stability 230
    6.6 Exercises 240
    References 241
    7 Protein Interactions 247
    7.1 Protein-protein interactions 247
    7.2 Protein-DNA interactions
    7.3 Protein-RNA interactions
    7.4 Protein-ligand interactions
    7.5 Quantitative structure activity relationship in protein-ligand interactions
    7.6 Exercises
    References
    Appendix A 303
    List of protein databases
    List of protein Web servers
    Index 313