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Rational Drug Design

  • Book
  • © 1999

Overview

Editors:
  1. Donald G. Truhlar

    1. Department of Chemistry, University of Minnesota, Minneapolis, USA

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  2. W. Jeffrey Howe

    1. Pharmacia & Upjohn Inc., Kalamazoo, USA

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  3. Anthony J. Hopfinger

    1. Department of Medicinal Chemistry and Pharmacognocy, College of Pharmacy, University of Illinois at Chicago, Chicago, USA

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  4. Jeff Blaney

    1. Metaphorics LLC, Piedmont, USA

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  5. Richard A. Dammkoehler

    1. Department of Computer Science, Washington University, St. Louis, USA

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Part of the book series: The IMA Volumes in Mathematics and its Applications (IMA, volume 108)

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Table of contents (14 chapters)

  1. Front Matter

    Pages i-xii
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  2. Panel Discussions

    1. Panel Discussion: Important Current Problems in Drug Design that may be Computationally Tractable

      • Dave Doherty, Bill Dunn, Graham Richards, Doug Rohrer, A. J. Hopfinger, W. J. Howe
      Pages 1-6

    2. Panel Discussion: New Problems that Should be Addressed in the Next Ten Years

      • Gordon Crippen, Simon Kearsley, Garland Marshall, Phil Portoghese, Jeff Blaney
      Pages 7-9

  3. Molecular Properties

    1. Matching of Chemical and Biological Structures Using Subgraph and Maximal Common Subgraph Isomorphism Algorithms

      • Peter Willett
      Pages 11-38

    2. Molecular Similarity

      • W. Graham Richards, Daniel D. Robinson
      Pages 39-49

    3. Modeling The Effect of Solvation on Structure, Reactivity, and Partitioning of Organic Solutes: Utility in Drug Design

      • Candee C. Chambers, David J. Giesen, Gregory D. Hawkins, Christopher J. Cramer, Donald G. Truhlar, Wouter H. J. Vaes
      Pages 51-72

    4. Cell-Based Methods for Sampling in High-Dimensional Spaces

      • Jason A. Rush
      Pages 73-79

    5. A Preliminary Multiobjective Analysis of the Chemotherapeutic Benefits of Hairpin-Linked Polyamides

      • Wynn L. Walker, David S. Goodsell, Richard E. Dickerson, Elliot M. Landaw
      Pages 81-92

  4. Receptor-Based Modeling

    1. Using Structural Information for the Creative Design of Molecules

      • Colin McMartin, Regine S. Bohacek
      Pages 93-101

    2. Growmol, A De novo Computer Program, and its Application to Thermolysin and Pepsin: Results of the Design and Synthesis of a Novel Inhibitor

      • Regine Bohacek, Colin Mcmartin, Peter Glunz, Daniel H. Rich
      Pages 103-114

    3. Deducing Objective Site Models by Mixed Integer Programming

      • Gordon M. Crippen
      Pages 115-126

  5. Numerical Methods

    1. Molecular Dynamics Information Extraction

      • Dennis Sprous, Weidong Wang, Ganesan Ravishanker, Matthew A. Young, David L. Beveridge
      Pages 127-147

    2. Ionic Charging Free Energies Using Ewald Summation

      • Tom Darden
      Pages 149-161

    3. Genetic Function Approximation: Evolutionary Construction of Novel, Interpretable, Nonlinear Models of Experimental Data

      • David Rogers
      Pages 163-189

    4. Applications of Distributed Computing to Conformational Searches

      • Brian T. Luke
      Pages 191-206

  6. Back Matter

    Pages 207-213
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Keywords

About this book

Drug research and discovery are of critical importance in human health care. Computational approaches for drug lead discovery and optimization have proven successful in many recent research programs. These methods have grown in their effectiveness not only because of improved understanding of the basic science - the biological events and molecular interactions that define a target for therapeutic intervention - but also because of advances in algorithms, representations, and mathematical procedures for studying such processes. This volume surveys some of those advances. A broad landscape of high-profile topics in computer-assisted molecular design (CAMD) directed to drug design are included. Subject areas represented in the volume include receptor-based applications such as binding energy approximations, molecular docking, and de novo design; non-receptor-based applications such as molecular similarity; molecular dynamics simulations; solvation and partitioning of a solute between aqueous and nonpolar media; graph theory; non-linear multidimensional optimization, processing of information obtained from simulation studies, global optimization and search strategies, and performance enhancement through parallel computing.

Editors and Affiliations

  • Department of Chemistry, University of Minnesota, Minneapolis, USA

    Donald G. Truhlar

  • Pharmacia & Upjohn Inc., Kalamazoo, USA

    W. Jeffrey Howe

  • Department of Medicinal Chemistry and Pharmacognocy, College of Pharmacy, University of Illinois at Chicago, Chicago, USA

    Anthony J. Hopfinger

  • Metaphorics LLC, Piedmont, USA

    Jeff Blaney

  • Department of Computer Science, Washington University, St. Louis, USA

    Richard A. Dammkoehler

Bibliographic Information

  • Book Title: Rational Drug Design

  • Editors: Donald G. Truhlar, W. Jeffrey Howe, Anthony J. Hopfinger, Jeff Blaney, Richard A. Dammkoehler

  • Series Title: The IMA Volumes in Mathematics and its Applications

  • DOI: https://doi.org/10.1007/978-1-4612-1480-9

  • Publisher: Springer New York, NY

  • eBook Packages: Springer Book Archive

  • Copyright Information: Springer Science+Business Media New York 1999

  • Hardcover ISBN: 978-0-387-98753-8Published: 12 March 1999

  • Softcover ISBN: 978-1-4612-7159-8Published: 08 October 2012

  • eBook ISBN: 978-1-4612-1480-9Published: 06 December 2012

  • Series ISSN: 0940-6573

  • Series E-ISSN: 2198-3224

  • Edition Number: 1

  • Number of Pages: XII, 213

  • Topics: Numerical Analysis, Mathematical and Computational Biology

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