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Protein-Ligand Interactions and Drug Design

  • Book
  • © 2021

Overview

Editors:
  1. Flavio Ballante

    1. Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden

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  • 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 2266)

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Table of contents (18 protocols)

  1. Front Matter

    Pages i-xv
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  2. Chemical Space

    1. Front Matter

      Pages 1-1
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    2. Investigation of the Click-Chemical Space for Drug Design Using ZINClick

      • Alberto Massarotti
      Pages 3-10

    3. Molecular Scaffold Hopping via Holistic Molecular Representation

      • Francesca Grisoni, Gisbert Schneider
      Pages 11-35

  3. Hit Identification and Hit-to-Lead Optimization

    1. Front Matter

      Pages 37-37
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    2. Biased Docking for Protein–Ligand Pose Prediction

      • Juan Pablo Arcon, Adrián G. Turjanski, Marcelo A. Martí, Stefano Forli
      Pages 39-72

    3. Binding Mode Prediction and Virtual Screening Applications by Covalent Docking

      • Andrea Scarpino, György G. Ferenczy, György M. Keserű
      Pages 73-88

    4. Ligand–Receptor Interactions and Drug Design

      • Aggeliki Syriopoulou, Ioannis Markopoulos, Andreas G. Tzakos, Thomas Mavromoustakos
      Pages 89-104

    5. Simulation of Ligand Transport in Receptors Using CaverDock

      • Jana Hozzová, Ondřej Vávra, David Bednář, Jiří Filipovič
      Pages 105-124

    6. Negative Image-Based Screening: Rigid Docking Using Cavity Information

      • Pekka A. Postila, Sami T. Kurkinen, Olli T. Pentikäinen
      Pages 125-140

    7. Negative Image-Based Rescoring: Using Cavity Information to Improve Docking Screening

      • Olli T. Pentikäinen, Pekka A. Postila
      Pages 141-154

    8. Fragment-Based Drug Design of Selective HDAC6 Inhibitors

      • Dusan Ruzic, Nemanja Djokovic, Katarina Nikolic
      Pages 155-170

    9. A Protocol to Use Comparative Binding Energy Analysis to Estimate Drug-Target Residence Time

      • Gaurav K. Ganotra, Ariane Nunes-Alves, Rebecca C. Wade
      Pages 171-186

    10. Dynamic Docking Using Multicanonical Molecular Dynamics: Simulating Complex Formation at the Atomistic Level

      • Gert-Jan Bekker, Narutoshi Kamiya
      Pages 187-202

    11. Free Energy Calculations for Protein–Ligand Binding Prediction

      • Willem Jespers, Johan Åqvist, Hugo Gutiérrez-de-Terán
      Pages 203-226

    12. Exploiting Water Dynamics for Pharmacophore Screening

      • David Schaller, Szymon Pach, Marcel Bermudez, Gerhard Wolber
      Pages 227-238

    13. Markov State Models to Elucidate Ligand Binding Mechanism

      • Yunhui Ge, Vincent A. Voelz
      Pages 239-259

  4. Drug Repurposing, Polypharmacology, and Target Identification

    1. Front Matter

      Pages 261-261
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    2. From Homology Modeling to the Hit Identification and Drug Repurposing: A Structure-Based Approach in the Discovery of Novel Potential Anti-Obesity Compounds

      • Giosuè Costa, Anna Artese, Francesco Ortuso, Stefano Alcaro
      Pages 263-277

    3. Multiple Target Drug Design Using LigBuilder 3

      • Xiaoyu Qing, Shiwei Wang, Yaxia Yuan, Jianfeng Pei, Luhua Lai
      Pages 279-298
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Keywords

About this book

This detailed book collects modern and established computer-based methods aimed at addressing the drug discovery challenge from disparate perspectives by exploiting information on ligand-protein recognition. Beginning with methods that allow for the exploration of specific areas of chemical space and the designing of virtual libraries, the volume continues with sections on methods based on docking, quantitative models, and molecular dynamics simulations, which are employed for ligand discovery or development, as well as methods exploiting an ensemble of protein structures for the identification of potential protein targets. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. 

Authoritative and cutting-edge, Protein-Ligand Interactions and Drug Design provides detailed practical procedures of solid computer-aided drug design methodologies employed to rationalize and optimize protein-ligand interactions, for experienced researchers and novices alike.

Editors and Affiliations

  • Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden

    Flavio Ballante

About the editor

Flavio Ballante is a researcher in the Department of Cell and Molecular Biology at Uppsala University (Sweden). He graduated in Medicinal Chemistry from Sapienza University in Rome (Italy) where he also obtained a Ph.D. in Pharmaceutical Sciences. During his academic career, he conducted research in France (University of Lorraine, Metz), the USA (Washington University School of Medicine in St. Louis, MO), and Sweden (Uppsala University, Uppsala), working on computer-aided drug design, chemistry, and biology experiments. His primary research goals are directed toward understanding the basis for molecular recognition at the atomic level, and his scientific activity is mainly focused on the design, development, and application of computational methods for ligand discovery.

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