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Docking Screens for Drug Discovery

  • Book
  • © 2019

Overview

Editors:
  1. Walter Filgueira de Azevedo Jr.

    1. Escola de Ciências da Saúde, Pontifícia Universidade Católica do Rio Grande do Sul—PUCRS, Porto Alegre, Brazil

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    You can also search for this editor in PubMed   Google Scholar

  • Includes cutting-edge techniques
  • Provides step-by-step detail essential for reproducible results
  • Contains key implementation advice from the experts

Part of the book series: Methods in Molecular Biology (MIMB, volume 2053)

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Table of contents (17 protocols)

  1. Front Matter

    Pages i-xvii
    Download chapter PDF

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

    • Maciej Wójcikowski, Pawel Siedlecki, Pedro J. Ballester
    Pages 1-12

  3. Integrating Molecular Docking and Molecular Dynamics Simulations

    • Lucianna H. S. Santos, Rafaela S. Ferreira, Ernesto R. Caffarena
    Pages 13-34

  4. How Docking Programs Work

    • Gabriela Bitencourt-Ferreira, Walter Filgueira de Azevedo Jr.
    Pages 35-50

  5. SAnDReS: A Computational Tool for Docking

    • Gabriela Bitencourt-Ferreira, Walter Filgueira de Azevedo Jr.
    Pages 51-65

  6. Electrostatic Energy in Protein–Ligand Complexes

    • Gabriela Bitencourt-Ferreira, Martina Veit-Acosta, Walter Filgueira de Azevedo Jr.
    Pages 67-77

  7. Van der Waals Potential in Protein Complexes

    • Gabriela Bitencourt-Ferreira, Martina Veit-Acosta, Walter Filgueira de Azevedo Jr.
    Pages 79-91

  8. Hydrogen Bonds in Protein-Ligand Complexes

    • Gabriela Bitencourt-Ferreira, Martina Veit-Acosta, Walter Filgueira de Azevedo Jr.
    Pages 93-107

  9. Molecular Dynamics Simulations with NAMD2

    • Gabriela Bitencourt-Ferreira, Walter Filgueira de Azevedo Jr.
    Pages 109-124

  10. Docking with AutoDock4

    • Gabriela Bitencourt-Ferreira, Val Oliveira Pintro, Walter Filgueira de Azevedo Jr.
    Pages 125-148

  11. Molegro Virtual Docker for Docking

    • Gabriela Bitencourt-Ferreira, Walter Filgueira de Azevedo Jr.
    Pages 149-167

  12. Docking with GemDock

    • Gabriela Bitencourt-Ferreira, Walter Filgueira de Azevedo Jr.
    Pages 169-188

  13. Docking with SwissDock

    • Gabriela Bitencourt-Ferreira, Walter Filgueira de Azevedo Jr.
    Pages 189-202

  14. Molecular Docking Simulations with ArgusLab

    • Gabriela Bitencourt-Ferreira, Walter Filgueira de Azevedo Jr.
    Pages 203-220

  15. Web Services for Molecular Docking Simulations

    • Nelson J. F. da Silveira, Felipe Siconha S. Pereira, Thiago C. Elias, Tiago Henrique
    Pages 221-229

  16. Homology Modeling of Protein Targets with MODELLER

    • Gabriela Bitencourt-Ferreira, Walter Filgueira de Azevedo Jr.
    Pages 231-249

  17. Machine Learning to Predict Binding Affinity

    • Gabriela Bitencourt-Ferreira, Walter Filgueira de Azevedo Jr.
    Pages 251-273

  18. Exploring the Scoring Function Space

    • Gabriela Bitencourt-Ferreira, Walter Filgueira de Azevedo Jr.
    Pages 275-281

  19. Back Matter

    Pages 283-286
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Keywords

About this book

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.

Editors and Affiliations

  • Escola de Ciências da Saúde, Pontifícia Universidade Católica do Rio Grande do Sul—PUCRS, Porto Alegre, Brazil

    Walter Filgueira de Azevedo Jr.

Bibliographic Information

  • Book Title: Docking Screens for Drug Discovery

  • Editors: Walter Filgueira de Azevedo Jr.

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-4939-9752-7

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media, LLC, part of Springer Nature 2019

  • Hardcover ISBN: 978-1-4939-9751-0Published: 27 August 2019

  • Softcover ISBN: 978-1-4939-9754-1Published: 27 August 2020

  • eBook ISBN: 978-1-4939-9752-7Published: 26 August 2019

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XVII, 286

  • Number of Illustrations: 153 b/w illustrations, 10 illustrations in colour

  • Topics: Pharmacology/Toxicology, Protein-Ligand Interactions, Computer Appl. in Life Sciences

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