Part I: Drug Binding Site Prediction, Design, and Descriptors
1. A Molecular Dynamics Ensemble-based Approach for the Mapping of Druggable Binding Sites
Anthony Ivetac and J, Andrew McCammon
2. Analysis of Protein Binding Sites by Computational Solvent Mapping
David R. Hall, Dima Kozakov, and Sandor Vajda
3. Evolutionary Trace for Prediction and Redesign of Protein Functional Sites
Angela Wilkins, Serkan Erdin, Rhonald Lua, and Olivier Lichtarge
4. Information Entropic Function for Molecular Descriptor Profiling
Anne Mai Wasswrmann, Britta Nisius, Martin Vogt, and
Jürgen Bajorath
Part II: Virtual Screening of Large Compound Libraries: Including Molecular Flexibility
5. Expanding the Conformational Selection Paradigm in Protein-Ligand Docking
Guray Kuzu, Ozlem Keskin, Attila Gursoy, and Ruth Nussinov
6. Flexibility Analysis of Biomacromolecules with Application to Computer-aided Drug Design
Simone Fulle and Holger Gohlke
7.On the Use of Molecular Dynamics Receptor Conformations for Virtual Screening
Sara Nichols, Riccardo Baron, and J. Andrew McCammon
8. Virtual Ligand Screening Against Comparative Protein Structure Models
Hao Fan, John J. Irwin, and Andrej Sali
9.AMMOS Software: Method and Application
Tania Pencheva, David Lagorce, Ilza Pajeva, Bruno O. Villoutreix, and Maria A. Miteva
10.Rosetta Ligand Docking with Flexible XML Protocols
Gordon Lemmon and Jens Meiler
11.Normal Mode-Based Approaches in Receptor Ensemble Docking
Claudio N. Cavasotto
12. Application of Conformational Clustering in Protein-Ligand Docking
Giovanni Bottegoni, Walter Rocchia, and Andrea Cavalli
13. How to Benchmark Methods for Structure-based Virtual Screenin of Large Compound Libraries
Andrew J. Christofferson and Niu Huang
Part III: Prediction of Protein-Protein Docking and Interactions
14. AGGRESCAN: Method, Application, and Perspectives for Drug Design
Natalia S. de Groot, Virginia Castillo, Ricardo Graña, and Salvador Ventura Zamora
15. ATTRACT and PTOOLS: Open Source Programs for Protein-protein Docking
Sebastian Schneider, Adrien Saladin, Chantal Prevost, and Martin Zacharias
16. Prediction of Interacting Protein Residues using Sequence and Structure Data
Vedran Franke, Mile Sikic, and Kristian Vlahovicek
