Homology Modeling, 2012
Methods and Protocols
Methods in Molecular Biology Series, Vol. 857

Knowledge about protein tertiary structure can guide experiments, assist in the understanding of structure-function relationships, and aid the design of new therapeutics for disease. Homology modeling is an in silico method that predicts the tertiary structure of an amino acid sequence based on a homologous experimentally determined structure.  In, Homology Modelling: Methods and Protocols experts in the field describe each homology modeling step from first principles, provide case studies for challenging modeling targets and describe methods for the prediction of how other molecules such as drugs can interact with the protein. Written in the highly successful Methods in Molecular Biology? series format, the chapters include the kind of detailed description and implementation advice that is crucial for getting optimal results in the laboratory.

Thorough and intuitive, Homology Modelling: Methods and Protocols guides scientists in the available homology modeling methods.

Classification of Proteins: Available Structural Space for MolecularModelling.-Effective Techniques for Protein Structure Mining.-Methods for Sequence-structure Alignment.-Force Fields for Homology Modeling.-Automated Protein Structure Modeling with SWISS-MODEL Workspace and the Protein Model Portal.-A Practical Introduction to Molecular Dynamics Simulations: Applications to Homology Modeling.-Methods for Accurate Homology Modeling by Global Optimization.-Ligand-Guided Receptor Optimization.-Loop Simulations.-Methods of Protein Structure Comparison.- Homology Modeling of Class A G Protein-Coupled Receptors.-Homology Modeling of Transporter Proteins (Carriers and Ion Channels).-Methods for the Homology Modeling of Antibody Variable Regions.-Investigating Protein Variants using Structural Calculation Techniques.-Macromolecular Assembly Structures by Comparative Modeling and Electron Microscopy.-Preparation and Refinement of Model Protein-Ligand Complexes.-Modeling Peptide-protein Interactions.-Comparison of Common Homology Modeling Algorithms: Application of User-defined Alignments.