Homology modeling : methods and protocols / edited by Andrew J. W. Orry, Ruben Abagyan. — New York : Humana Press :Springer, c2012. – (58.17/M592/v.857)

Contents

    CONTENTS
    
    Preface
    Contributors
    1 Classification of Proteins: Available Structural Space for Molecular Modeling
    2 Effective Techniques for Protein Structure Mining 33
    3 Methods for Sequence-Structure Alignment
    4 Force Fields for Homology Modeling 83
    5 Automated Protein Structure Modeling with SWISS-MODEL Workspace and the Protein Model Portal 107
    6 A Practical Introduction to Molecular Dynamics Simulations: Applications to Homology Modeling 137
    7 Methods for Accurate Homology Modeling by Global Optimization.
    8 Ligand-Guided Receptor Optimization 189
    9 Loop Simulations 207
    10 Methods of Protein Structure Comparison 231
    11 Homology Modeling of Class A G Protein-Coupled Receptors 259
    12 Homology Modeling of Transporter Proteins (Carriers and Ion Channels) 281
    13 Methods for the Homology Modeling of Antibody Variable Regions.
    14 Investigating Protein Variants Using Structural Calculation Techniques 313
    15 Macromolecular Assembly Structures by Comparative Modeling and Electron Microscopy 331
    16 Preparation and Refinement of Model Protein-Ligand Complexes 351
    17 Modeling Peptide-Protein Interactions 375
    18 Comparison of Common Homology Modeling Algorithms: Application of User-Defined Alignments 399
    Index 415