Handbook of Chemoinformatics: From Data to Knowledge

Contents
Volume 1
Foreword xluii
Preface xlix
Contributors liii
Introduction 1
The Scope o f Chemoinformatics 3
Johann Casteiger
Textbook-Handbook 4
References 5
A History of Chemoinformatics 6
Peter Willett
Introduction 6
The Early Days: Representations and Structure Searching
The Early Days: Substructure Searching
Similarity Searching, Clustering, and Diversity Analysis
Searching Databases of Patents 11
Searching Databases of Reactions and Synthesis Design
Computer-aided Structure Elucidation 13
3D Substructure Searching 13
QSAR and Docking 14
Conclusions 16
References 16
Representation of Chemical Compounds 21
Introduction 23
Representation of Molecular Structures - Overview
John M. Barnard
Introduction 27
History 28

Chemical Nomenclature and Structure Representation: Algorithmic Generation and Conversion 51
SMILES - A Language for Molecules and Reactions
Graph Theory in Chemistry 103
Processing Constitutional Information 139
Canonical Numbering and Constitutional Symmetry Ring Perception 161
Topological Structure Generators 178
Cornbinatorics of Organic Molecular Structures
Representation and Manipulation of Stereochemistry
Representation of 3D Structures 231
3D Structure Generation 231
Conformational Analysis and Searching 262
Molecular Shape Analysis 302
Computer Visualization of Molecular Models - Tools for Man-Machine Communication in Molecular Science 320
Representation of Chemical Reactions 345
Reaction Classification and Knowledge Acquisition
The Data 389
Data Types 392
Quality Control and Data Analysis
Experimental Design 423
Standard Exchange Formats for Spectral Data
XML and Its Application in Chemistry
DatabasesIData Sources 491
Overview of DatabasesIData Sources 496
Bibliographic Databases 507
Databases of Chemical Structures 523
The CAS Information System: Applying Scientific Knowledge and Technology for Better Information 556
The Beilstein Database 608
Databases in Inorganic Chemistry 629
The Cambridge Structural Database (CSD) of Small Molecule Crystal Structures 645
Databases of Chemical Reactions 667
Spectroscopic Databases 700
Databases on Environmental Information 722
Patent Databases 743
Databases in Biochemistry and Molecular Biology
Chemistry on the Internet 794
Laboratory Information Management Systems (LIMS)
Searching Chemical Structures
Current State of the Art o f Markush Topological Search Systems
Similarity Searching in Chemical Structure Databases
Calculation of Physical and Chemical Data
Molecular Mechanics 920
Quantum Mechanics 947
Descriptors for Chemical Compounds 977
Topological Indices 981
Descriptors from Molecular Geometry 1004
A Hierarchy of Structure Representations
Representation of Molecular Chirality
Machine Learning Techniques in Chemistry
Multivariate Data Analysis in Chemistry
Partial Least Squares (PLS) in Cheminformatics
Neural Networks 11 67
Fuzzy Set Theory and Fuzzy Logic and Its Application to Molecular
Recognition 1216
Evolutionary Algorithms and their Applications in Chemistry

Expert Systems 1281
Prediction of Physical and Chemical Properties 1300
Quantitative Structure-Property Relationships 1314
Web-Based Calculation of Molecular Properties

Structure-Spectra Correlations 1349
Correlations between Chemical Structure and Infrared Spectra
Correlations between Chemical Structures and NMR Data
Computer-Assisted Structure Elucidation

Chemical Reactions and Synthesis Design
Computer-Assisted Synthesis Design (CASD) 1428
Computer-Assisted Synthesis Design by WODCA (CASD)

Drug Design 1508
Chernoinforrnatics and the Quest for Leads in Drug Discovery
QSAR in Drug Design 1532
Comparative Molecular Field Analysis (CoMFA)
3D- and nD-QSAR Methods 1576
High-Throughput Chemistry 1604
Molecular Diversity 1640
Pharmacophore and Drug Discovery 1687
De-Novo Design Systems 1712
The Docking Problem 1732
From Structural Genomics to Drug Design: Knowledge Discovery in Crystallographic Databases to Assist Lead Discovery and Optimization 17G9

Chemoinformatics/Bioinformatics 1789
Prediction o f Protein Structure Through Evolution
Sequence and Genome Bioinformatics 1812
Future Directions 1845
Index 1849

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