About the Book
1. Classification of Proteins: Available Structural Space for Molecular Modelling
Antonina Andreeva
2. Effective Techniques for Protein Structure Mining
Stefan J. Suhrer, Markus Gruber, Markus Wiederstein, Manfred J. Sippl
3. Methods for Sequence-Structure Alignment
Česlovas Venclovas
4. Force Fileds for Homology Modeling
Andrew J. Bordner
5. Automated Protein Structure Modeling with SWISS-MODELWorkspace and the Protein Model Portal
Lorenza Bordoli and Torsten Schwede
6. A Practical Introduction to Molecular Dynamics Simulations: Applications to Homology Modeling
Alessandra Nurisso, Antoine Daina and Ross C. Walker
7. Methods for Accurate Homology Modeling by Global Optimization
Keehyoung Joo, Jinwoo Lee, Jooyoung Lee
8. Ligand- Guided Receptor Optimization
Vsevolod Katritch, Manuel Rueda, Ruben Abagyan
9. Loop Simulations
Maxim Totrov
10. Methods of Protein Structure Comparison
Irina Kufareva and Ruben Abagyan
11. Homology Modeling of Class A G Protein-Coupled Receptors
Stefano Costanzi
12. Homology Modeling of Transporter Proteins (Carriers and Ion Channels)
Aina Westrheim Ravna and Ingebrigy Sylte
13. Methods for the Homology Modeling of Antibody Variable Regions
Aroop Sircar
14. Investigation Protein Variants using Structural Calculation Techniques
Jonas Carlsson and Bengt Persson
15. Macromolecular Assembly Structures by Comparative Modeling and Electron Microscopy
Keren Lasker, Javier A. Velázquez-Muriel, Benjamin M. Webb, Zheng Yang, Thomas E. Ferrin, and Andrej Sali
16. Preparation and Refinement of Model Protein-Ligand Complexes
Andrew J.W. Orry and Ruben Abagyan
17. Modeling Peptide-protein Interactions
Nir London, Barak Raveh, Ora Schueler-Furman
18. Comparison of Common Homology Modeling Algorithms: Applications of User-defined Alignments
Michael A. Dolan, James W. Noah, and Darrell Hurt
