Homology Modeling: Methods and Protocols

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

Ceslovas 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