Virtual Screening

Frontmatter......Page 1
Contents......Page 6
List of Contributors......Page 16
Preface......Page 21
A Personal Foreword......Page 23
Part One
Principles......Page 29
1. Virtual Screening of Chemical Space: From Generic Compound Collections to Tailored Screening Libraries......Page 30
2. Preparing and Filtering Compound Databases for Virtual and Experimental Screening......Page 61
3. Ligand-Based Virtual Screening......Page 86
4. The Basis for Target-Based Virtual Screening: Protein Structures......Page 111
5. Pharmacophore Models for Virtual Screening......Page 139
6. Docking Methods for Virtual Screening: Principles and Recent Advances......Page 177
Part Two
Challenges......Page 201
7. The Challenge of Affinity Prediction: Scoring Functions for Structure-Based Virtual Screening......Page 202
8. Protein Flexibility in Structure-Based Virtual Screening: From Models to Algorithms......Page 245
9. Handling Protein Flexibility in Docking and High-Throughput Docking: From Algorithms to Applications......Page 267
10. Consideration of Water and Solvation Effects in Virtual Screening......Page 285
Part Three
Applications and Practical Guidelines......Page 312
11. Applied Virtual Screening: Strategies, Recommendations, and Caveats......Page 313
12. Applications and Success Stories in Virtual Screening......Page 339
Part Four
Scenarios and Case Studies: Routes to Success......Page 379
13. Scenarios and Case Studies: Examples for Ligand-Based Virtual Screening......Page 380
14. Virtual Screening on Homology Models......Page 399
15. Target-Based Virtual Screening on Small-Molecule Protein Binding Sites......Page 429
16. Target-Based Virtual Screening to Address Protein–Protein Interfaces......Page 453
17. Fragment-Based Approaches in Virtual Screening......Page 484
Appendix A: Software Overview......Page 507
Appendix B: Virtual Screening Application Studies......Page 516
Index......Page 525