Main description:

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.

Contents:

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

Maciej Wojcikowski, 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.