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This book focuses on recent developments in docking simulations for target proteins with chapters on specific techniques or applications for docking simulations, including the major docking programs. Additionally, the volume explores the scoring functions developed for the analysis of docking results and to predict ligand-binding affinity as well as the importance of docking simulations for the initial stages of drug discovery. Written for the highly successful Methods in Molecular Biology series, this collection presents the kind of detail and key implementation advice to ensure successful results. 
Authoritative and practical, Docking Screens for Drug Discovery aims to serve those interested in molecular docking simulation and also in the application of these methodologies for drug discovery.

Docking Screens for Drug Discovery

1. Building Machine-Learning Scoring Functions for Structure-Based Prediction of Intermolecular Binding Affinity

            Maciej Wójcikowski, Pawel Siedlecki, and Pedro J. Ballester

 

2. Integrating Molecular Docking and Molecular Dynamics Simulations

            Lucianna H.S. Santos, Rafaela S. Ferreira, and Ernesto R. Caffarena

 

3. How Docking Programs Work

            Gabriela Bitencourt-Ferreira and Walter Filgueira de Azevedo Jr.

 

4. SAnDReS: A Computational Tool for Docking

            Gabriela Bitencourt-Ferreira and Walter Filgueira de Azevedo Jr.

 

5. Electrostatic Energy in Protein-Ligand Complexes

            Gabriela Bitencourt-Ferreira, Martina Veit-Acosta, and Walter Filgueira de Azevedo Jr.

 

6. Van der Waals Potential in Protein Complexes

            Gabriela Bitencourt-Ferreira, Martina Veit-Acosta, and Walter Filgueira de Azevedo Jr.

 

7. Hydrogen-Bonds in Protein-Ligand Complexes

            Gabriela Bitencourt-Ferreira, Martina Veit-Acosta, and Walter Filgueira de Azevedo Jr.

 

8. Molecular Dynamics Simulations with NAMD2

            Gabriela Bitencourt-Ferreira and Walter Filgueira de Azevedo Jr.

 

9. Docking with AutoDock4

            Gabriela Bitencourt-Ferreira, Val Oliveira Pinto, and Walter Filgueira de Azevedo Jr.

 

10. Molegro Virtual Docker for Docking

            Gabriela Bitencourt-Ferreira and Walter Filgueira de Azevedo Jr.

 

11. Docking with GemDock

            Gabriela Bitencourt-Ferreira and Walter Filgueira de Azevedo Jr.

 

12. Docking with SwissDock

            Gabriela Bitencourt-Ferreira and Walter Filgueira de Azevedo Jr.

 

13. Molecular Docking Simulations with ArgusLab

            Gabriela Bitencourt-Ferreira and Walter Filgueira de Azevedo Jr.

 

14. Web Services for Molecular Docking Simulations

            Nelson J.F. da Silveira, Felipe Siconha S. Pereira, Thiago C. Elias, and Tiago Henrique

 

15. Homology Modeling of Protein Targets with MODELLER

            Gabriela Bitencourt-Ferreira and Walter Filgueira de Azevedo Jr.

 

16. Machine Learning to Predict Binding Affinity

            Gabriela Bitencourt-Ferreira and Walter Filgueira de Azevedo Jr.

 

17. Exploring the Scoring Function Space

            Gabriela Bitencourt-Ferreira and Walter Filgueira de Azevedo Jr.