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  • © 2012

Computational Drug Discovery and Design

Editors:

  • Manual for state-of-the-art concepts and methodologies, as well as an advanced, specialized tool to design novel and orignial research for public health
  • Provides step-by-step detail essential for reproducible results
  • Contains key notes and implementaion advice from the experts

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

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Table of contents (36 protocols)

  1. Front Matter

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

    1. Front Matter

      Pages 1-1
    2. Analysis of Protein Binding Sites by Computational Solvent Mapping

      • David R. Hall, Dima Kozakov, Sandor Vajda
      Pages 13-27
    3. Evolutionary Trace for Prediction and Redesign of Protein Functional Sites

      • Angela Wilkins, Serkan Erdin, Rhonald Lua, Olivier Lichtarge
      Pages 29-42
    4. Information Entropic Functions for Molecular Descriptor Profiling

      • 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. Expanding the Conformational Selection Paradigm in Protein-Ligand Docking

      • Guray Kuzu, Ozlem Keskin, Attila Gursoy, Ruth Nussinov
      Pages 59-74
    3. On the Use of Molecular Dynamics Receptor Conformations for Virtual Screening

      • Sara E. Nichols, Riccardo Baron, J. Andrew McCammon
      Pages 93-103
    4. Virtual Ligand Screening Against Comparative Protein Structure Models

      • Hao Fan, John J. Irwin, Andrej Sali
      Pages 105-126
    5. AMMOS Software: Method and Application

      • T. Pencheva, D. Lagorce, I. Pajeva, B. O. Villoutreix, M. A. Miteva
      Pages 127-141
    6. Rosetta Ligand Docking with Flexible XML Protocols

      • Gordon Lemmon, Jens Meiler
      Pages 143-155
    7. Application of Conformational Clustering in Protein–Ligand Docking

      • Giovanni Bottegoni, Walter Rocchia, Andrea Cavalli
      Pages 169-186
  4. Prediction of Protein–Protein Docking and Interactions

    1. Front Matter

      Pages 197-197
  5. Prediction of Protein-Protein Docking and Interactions

    1. AGGRESCAN: Method, Application, and Perspectives for Drug Design

      • Natalia S. de Groot, Virginia Castillo, Ricardo Graña-Montes, Salvador Ventura
      Pages 199-220
    2. ATTRACT and PTOOLS: Open Source Programs for Protein–Protein Docking

      • Sebastian Schneider, Adrien Saladin, Sébastien Fiorucci, Chantal Prévost, Martin Zacharias
      Pages 221-232
    3. Prediction of Interacting Protein Residues Using Sequence and Structure Data

      • Vedran Franke, Mile Šikić, Kristian Vlahoviček
      Pages 233-251

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.

Reviews

From the reviews:

“Given that computational drug design is a rapidly expanding area of research, this book fills a niche that makes it useful for both novices and the more experienced in the field. … this is a practical manual, refitted with many protocols and examples, of how to employ the new techniques being developed by experts in the expanding field of computational drug discovery.” (Jed N. Lampe, Doody’s Book Reviews, July, 2012)

Editors and Affiliations

  • University of Utah, Salt Lake City, USA

    Riccardo Baron

Bibliographic Information

  • Book Title: Computational Drug Discovery and Design

  • Editors: Riccardo Baron

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-61779-465-0

  • Publisher: Humana Totowa, NJ

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media 2012

  • Hardcover ISBN: 978-1-61779-464-3Published: 21 December 2011

  • Softcover ISBN: 978-1-4939-6227-3Published: 23 August 2016

  • eBook ISBN: 978-1-61779-465-0Published: 21 December 2011

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XVII, 628

  • Topics: Pharmacology/Toxicology

Buy it now

Buying options

eBook USD 129.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book USD 169.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book USD 219.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Other ways to access