Computational Drug Discovery and Design

  • Riccardo Baron

Part of the Methods in Molecular Biology book series (MIMB, volume 819)

Table of contents

  1. Front Matter
    Pages i-xvii
  2. Drug Binding Site Prediction, Design, and Descriptors

    1. Front Matter
      Pages 1-1
    2. David R. Hall, Dima Kozakov, Sandor Vajda
      Pages 13-27
    3. Angela Wilkins, Serkan Erdin, Rhonald Lua, Olivier Lichtarge
      Pages 29-42
    4. Anne Mai Wassermann, Britta Nisius, Martin Vogt, Jürgen Bajorath
      Pages 43-55
  3. Virtual Screening of Large Compound Libraries: Including Molecular Flexibility

    1. Front Matter
      Pages 57-57
    2. Guray Kuzu, Ozlem Keskin, Attila Gursoy, Ruth Nussinov
      Pages 59-74
    3. Sara E. Nichols, Riccardo Baron, J. Andrew McCammon
      Pages 93-103
    4. Hao Fan, John J. Irwin, Andrej Sali
      Pages 105-126
    5. T. Pencheva, D. Lagorce, I. Pajeva, B. O. Villoutreix, M. A. Miteva
      Pages 127-141
    6. Gordon Lemmon, Jens Meiler
      Pages 143-155
    7. Giovanni Bottegoni, Walter Rocchia, Andrea Cavalli
      Pages 169-186
  4. Prediction of Protein–Protein Docking and Interactions

    1. Front Matter
      Pages 197-197
    2. Natalia S. de Groot, Virginia Castillo, Ricardo Graña-Montes, Salvador Ventura
      Pages 199-220
    3. Sebastian Schneider, Adrien Saladin, Sébastien Fiorucci, Chantal Prévost, Martin Zacharias
      Pages 221-232
    4. Vedran Franke, Mile Šikić, Kristian Vlahoviček
      Pages 233-251
  5. Rescoring Docking Predictions

    1. Front Matter
      Pages 253-253
    2. Cristiano R. W. Guimarães
      Pages 255-268
    3. Zunnan Huang, Chung F. Wong
      Pages 269-293
    4. Traian Sulea, Enrico O. Purisima
      Pages 295-303
    5. Hugo Gutiérrez-de-Terán, Johan Åqvist
      Pages 305-323
  6. Crucial Neglected Effects: Entropy, Solvent, and Protonation

    1. Front Matter
      Pages 325-325
    2. Panagiotis L. Kastritis, Aalt D. J. van Dijk, Alexandre M. J. J. Bonvin
      Pages 355-374
    3. Arianna Fornili, Flavia Autore, Nesrine Chakroun, Pierre Martinez, Franca Fraternali
      Pages 375-392
    4. Zheng Li, Themis Lazaridis
      Pages 393-404
    5. Elmar Krieger, Roland L. Dunbrack Jr., Rob W. W. Hooft, Barbara Krieger
      Pages 405-421
  7. Toward the Use of Robust Free Energy Methods in Drug Design

  8. Biomedical Applications

    1. Front Matter
      Pages 525-525
    2. William Sinko, Emma Sierecki, César A. F. de Oliveira, J. Andrew McCammon
      Pages 561-573
    3. Rommie E. Amaro, Wilfred W. Li
      Pages 575-594
    4. Chia-en A. Chang, Rizi Ai, Michael Gutierrez, Michael J. Marsella
      Pages 595-613
  9. Back Matter
    Pages 625-628

About this book


Due to the rapid and steady growth of available low-cost computer power, the use of computers for discovering and designing new drugs is becoming a central topic in modern molecular biology and medicinal chemistry. In Computational Drug Discovery and Design: Methods and Protocols expert researchers in the field provide key techniques to investigate biomedical applications for drug developments based on computational chemistry. These include methods and techniques from binding sites prediction to the accurate inclusion of solvent and entropic effects, from high-throughput screening of large compound databases to the expanding area of protein-protein inhibition, toward quantitative free-energy approaches in ensemble-based drug design using distributed computing. Written in the highly successful Methods in Molecular Biology™ series format, chapters include introductions to their respective topics, reference to software and open source analysis tools, step-by-step, readily reproducible computational protocols, and key tips on troubleshooting and avoiding known pitfalls.


Thorough and intuitive, Computational Drug Discovery and Design: Methods and Protocols aids scientists in the continuing study of state-of-the-art concepts and computer-based methodologies.


Computational Drug Design Computational Drug Discovery accurate inclusion of solvent binding sites prediction entropic effects medicinal chemistry molecular biology molecular dynamics simulation physics-based methodologies receptor-drug recognition

Editors and affiliations

  • Riccardo Baron
    • 1
  1. 1.University of UtahSalt Lake CityUSA

Bibliographic information

  • DOI
  • Copyright Information Springer Science+Business Media, LLC 2012
  • Publisher Name Springer, New York, NY
  • eBook Packages Springer Protocols
  • Print ISBN 978-1-61779-464-3
  • Online ISBN 978-1-61779-465-0
  • Series Print ISSN 1064-3745
  • Series Online ISSN 1940-6029
  • Buy this book on publisher's site
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