Handbook of Chemoinformatics: From Data to Knowledge in 4 Volumes

Copyright © 2003 WILEY-VCH Verlag GmbH & Co. KgaA

Handbook of Chemoinformatics: From Data to Knowledge in 4 Volumes

Editor(s): Johann Gasteiger

Published Online: 5 MAY 2008

Print ISBN: 9783527306800

Online ISBN: 9783527618279

DOI: 10.1002/9783527618279

About this Book

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Covering the application of computer-aided methods to chemical problems, such as structural databases, spectra interpretation, predicting chemical properties and molecular shapes, this four-volume work provides both newcomers and advanced users as well as lecturers with a profound and comprehensive overview of this increasingly important field.

Closely related to practice, this handbook leads readers step-by-step through:

  • Representation of molecular structures
  • Data types
  • Databases/Datasources
  • Search methods
  • Methods for data analysis
  • Applications

Table of contents

    1. You have free access to this content
      Frontmatter (pages 1–44)

    1. You have free access to this content
      Introduction (pages 1–2)

  3. Part I: Introduction

    1. Chapter I.1

      The Scope of Chemoinformatics (pages 3–5)

      Johann Gasteiger

    2. Chapter I.2

      A History of Chemoinformatics (pages 6–20)

      Peter Willett

  4. Part II: Representation of Chemical Compounds

    1. You have free access to this content
      Representation of Chemical Compounds (pages 21–26)

    2. Chapter II.1

      Representation of Molecular Structures-Overview (pages 27–50)

      John M. Barnard

    3. Chapter II.2

      Chemical Nomenclature and Structure Representation: Algorithmic Generation and Conversion (pages 51–79)

      Janusz Leon Wisniewski

    4. Chapter II.3

      SMILES-A Language for Molecules and Reactions (pages 80–102)

      David Weininger

    5. Chapter II.4

      Graph Theory in Chemistry (pages 103–138)

      Ovidiu Ivanciuc

    6. Chapter II.6

      Representation and Manipulation of Stereochemistry (pages 206–230)

      Bernhard Rohde

    7. Chapter II.8

      Molecular Shape Analysis (pages 302–319)

      Jarostaw Polanski

    8. Chapter II.9

      Computer Visualization of Molecular Models -Tools for Man-Machine Communication in Molecular Science (pages 320–344)

      Matthias Keil, Thorsten Borosch, Thomas E. Exner and Jürgen Brickmann

  5. Part II: Representation of Chemical Compounds - II.5 Processing Constitutional Information

    1. Chapter 5.1

      Canonical Numbering and Constitutional Symmetry (pages 139–160)

      Ovidiu Ivanciuc

    2. Chapter 5.2

      Ring Perception (pages 161–177)

      Geoffrey M. Downs

    3. Chapter 5.3

      Topological Structure Generators (pages 178–194)

      Ivan P. Bangov

    4. Chapter 5.4

      Combinatorics of Organic Molecular Structures (pages 195–205)

      David Weininger

  6. Part II: Representation of Chemical Compounds - II.7 Representation of 3D Structures

    1. Chapter 7.1

      3D Structure Generation (pages 231–261)

      Jens Sadowski

    2. Chapter 7.2

      Conformational Analysis and Searching (pages 262–301)

      Christof H. Schwab

  7. Part III: Representation of Chemical Reactions

    1. You have free access to this content
      Representation of Chemical Reactions (pages 345–347)

    2. Chapter III.1

      Reaction Classification and Knowledge Acquisition (pages 348–390)

      Lingran Chen

  8. Part IV: The Data

    1. You have free access to this content
      The Data (pages 389–391)

    2. Chapter IV.1

      Data Types (pages 392–409)

      Jarosew Tomczak

    3. Chapter 2.1

      Quality Control and Data Analysis (pages 410–422)

      David E. Booth, Thomas L Isenhour, John K. Mahaney, Michael Suh and Christine Wright

    4. Chapter 2.2

      Experimental Design (pages 423–445)

      Mario Marsili

    5. Chapter IV.3

      Standard Exchange Formats for Spectral Data (pages 446–465)

      Antony N. Davies

    6. Chapter IV.4

      XML and Its Application in Chemistry (pages 466–486)

      Peter Murray-Rust and Henry S. Rzepa

  9. Part V: Databases/Data Sources

    1. You have free access to this content
      Databases/Data Sources (pages 491–493)

    2. Chapter V.1

      Overview of Databases/Data Sources (pages 496–506)

      Gary D. Wiggins

    3. Chapter V.2

      Bibliographic Databases (pages 507–522)

      Andreas Barth

    4. Chapter V.3

      Databases of Chemical Structures (pages 523–555)

      C. Gregory

    5. Chapter V.4

      The CAS Information System: Applying Scientific Knowledge and Technology for Better Information (pages 556–607)

      William Fisanick and Eric R. Shively

    6. Chapter V.5

      The Beilstein Database (pages 608–628)

      Alexander J. Lawson

    7. Chapter V.6

      Databases in Inorganic Chemistry (pages 629–643)

      Jürgen Vogt, Natalja Vogt and Axel Schunk

    8. Chapter V.7

      The Cambridge Structural Database (CSD) of Small Molecule Crystal Structures (pages 645–666)

      Frank H. Allen, Karen J. Lipscomb and and Gary Battle

    9. Chapter V.8

      Databases of Chemical Reactions (pages 667–699)

      Engelbert Zass

    10. Chapter V.9

      Spectroscopic Databases (pages 700–721)

      Reinhard Neudert and Antony N. Davies

    11. Chapter V.10

      Databases on Environmental Information (pages 722–742)

      Kristina Voigt

    12. Chapter V.11

      Patent Databases (pages 743–755)

      Jürgen Vogt

    13. Chapter V.12

      Databases in Biochemistry and Molecular Biology (pages 756–793)

      Alexander Von Homeyer and Martin Reitz

    14. Chapter V.13

      Chemistry on the Internet (pages 794–843)

      Alexei Tarkhov

    15. Chapter V.14

      Laboratory Information Management Systems (LIMS) (pages 844–864)

      Markus Hemmer

  10. Part VI: Searching Chemical Structures

    1. You have free access to this content
      Searching Chemical Structures (pages 865–867)

    2. Chapter VI.1

      Two-Dimensional Structure and Substructure Searching (pages 868–884)

      Jun Xu

    3. Chapter VI.2

      Current State of the Art of Markush Topological Search Systems (pages 885–903)

      Andrew H. Berks

    4. Chapter VI.3

      Similarity Searching in Chemical Structure Databases (pages 904–912)

      Peter Willett

  11. Part VII: Calculation of Physical and Chemical Data

    1. You have free access to this content
      Calculation of Physical and Chemical Data (pages 917–919)

    2. Chapter VII.1

      Molecular Mechanics (pages 920–946)

      Harald Lanig

    3. Chapter VII.2

      Quantum Mechanics (pages 947–976)

      Tim Clark

  12. Part VIII: Descriptors for Chemical Compounds

    1. You have free access to this content
      Descriptors for Chemical Compounds (pages 977–979)

    2. Chapter VIII.1

      Topological Indices (pages 981–1003)

      Ovidiu Ivanciuc

    3. Chapter VIII.2

      Descriptors from Molecular Geometry (pages 1004–1033)

      Roberto Todeschini and Viviana Consonni

    4. Chapter VIII.3

      A Hierarchy of Structure Representations (pages 1034–1061)

      Johann Gasteiger

    5. Chapter VIII.4

      Representation of Molecular Chirality (pages 1062–1078)

      João Aires-De-Sousa

  13. Part IX: Methods for Data Analysis

    1. You have free access to this content
      Methods for Data Analysis (pages 1079–1081)

    2. Chapter IX.2

      Expert Systems (pages 1281–1294)

      Markus Hemmer

  14. Part IX: Methods for Data Analysis - IX.1 Inductive Learning Methods

    1. Chapter 1.1

      Machine Learning Techniques in Chemistry (pages 1082–1097)

      John R. Rose

    2. Chapter 1.2

      Multivariate Data Analysis in Chemistry (pages 1098–1133)

      Kurt Varmuza

    3. Chapter 1.3

      Partial Least Squares (PLS) in Cheminformatics (pages 1134–1166)

      Lennart Eriksson, Henrik Antti, Elaine Holmes, Erik Johansson, Torbjörn Lundstedt, John Shockcor and Svante Wold

    4. Chapter 1.4

      Neural Networks (pages 1167–1215)

      Jure Zupan

    5. Chapter 1.5

      Fuzzy Set Theory and Fuzzy Logic and Its Application to Molecular Recognition (pages 1216–1238)

      Thomas E. Exner, Matthias Keil and Jürgen Brickmann

    6. Chapter 1.6

      Evolutionary Algorithms and Their Applications in Chemistry (pages 1239–1280)

      Alexander Von Homeyer

  15. Part II: Applications

    1. You have free access to this content
      Applications (pages 1295–1299)

  16. Part X: Applications - X.1 Prediction of Physical and Chemical Properties

    1. Chapter 1.1

      Odanol/Water Partition Coefficients (pages 1300–1312)

      Raimund Mannhold

    2. Chapter 1.2

      Quantitative Structure-Property Relationships (pages 1314–1335)

      Peter C. Jurs

    3. Chapter 1.3

      Web-Based Calculation of Molecular Properties (pages 1336–1348)

      Peter Ertl and Paul Selzer

  17. Part X: Applications - X.2 Structure-Spectra Correlations

    1. Chapter 2.1

      Correlations between Chemical Structure and Infrared Spectra (pages 1349–1367)

      Paul Selzer

    2. Chapter 2.2

      Correlations between Chemical Structures and NMR Data (pages 1368–1377)

      Christoph Steinbeck

    3. Chapter 2.3

      Computer-Assisted Structure Elucidation (pages 1378–1406)

      Christoph Steinbeck

  18. Part X: Applications - X.3 Chemical Reactions and Synthesis Design

    1. Chapter 3.1

      Analysis of Reaction Information (pages 1407–1427)

      Guenter Grethe

    2. Chapter 3.2

      Computer-Assisted Synthesis Design (CASD) (pages 1428–1456)

      René Barone and Michel Chanon

    3. Chapter 3.3

      Computer-Assisted Synthesis Design by WODCA (CASD) (pages 1457–1507)

      M. Pförtner and M. Sitzmann

  19. Part X: Applications - X.4 Drug Design

    1. Chapter 4.1

      Chemoinformatics and the Quest for Leads in Drug Discovery (pages 1508–1531)

      Tudor I. Oprea

    2. Chapter 4.2

      QSAR in Drug Design (pages 1532–1554)

      Hugo Kubinyi

    3. Chapter 4.3

      Comparative Molecular Field Analysis (CoMFA) (pages 1555–1574)

      Hugo Kubinyi

    4. Chapter 4.4

      3D- and nD-QSAR Methods (pages 1576–1603)

      Emilio Xavier Esposito, Anton J. Hopfinger and Jeffry D. Madura

    5. Chapter 4.5

      High-Throughput Chemistry (pages 1604–1639)

      Wendy A. Warr

    6. Chapter 4.6

      Molecular Diversity (pages 1640–1686)

      Michael A. Farnum, Renée L Desjarlais and Dimitris K. Agrafiotis

    7. Chapter 4.7

      Pharmacophore and Drug Discovery (pages 1687–1711)

      Marc C. Nicklaus

    8. Chapter 4.8

      De-Novo Design Systems (pages 1712–1731)

      A. Peter Johnson

    9. Chapter 4.9

      The Docking Problem (pages 1732–1768)

      Christoph Sotriffer, Martin Stahl and Gerhard Klebe

    10. Chapter 4.10

      From Structural Genomics to Drug Design: Knowledge Discovery in Crystallographic Databases to Assist Lead Discovery and Optimization (pages 1769–1788)

      C. Klebe

  20. Part X: Applications - X.5 Chemoinformatics/Bioinformatics

    1. Chapter 5.1

      Prediction of Protein Structure Through Evolution (pages 1789–1811)

      Burkhard Rost, Jinfeng Liu, Dariusz Przybylski, Rajesh Nair, Kazimierz O. Wrzeszczynski, Henry Bigelow and Yanay Ofran

    2. Chapter 5.2

      Sequence and Genome Bioinformatics (pages 1812–1844)

      H. Werner Mewes

  21. Part XI: Future Directions

    1. Future Directions (pages 1845–1848)

      J. Gasteiger

    1. You have free access to this content
      Index (pages 1849–1870)

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