An Introduction to Chemoinformatics,9781402013478

An Introduction to Chemoinformatics

by ;
ISBN13: 9781402013478
ISBN10: 1402013477
Format: Hardcover
Pub. Date: 2003-07-01
Publisher(s): Kluwer Academic Pub
List Price: $125.99

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Summary

Chemoinformatics draws upon techniques from many disciplines including computer science, mathematics, computational chemistry and data visualisation to tackle these problems. This, the first text written specifically for this field, aims to provide an introduction to the major techniques of chemoinformatics. The first part of the book deals with the representation of 2D and 3D molecular structures, the calculation of molecular descriptors and the construction of mathematical models. The second part describes other important topics including molecular similarity and diversity, the analysis of large data sets, virtual screening, and library design. Simple illustrative examples are used throughout to illustrate key concepts, supplemented with case studies from the literature. The book is aimed at graduate students, final-year undergraduates, and professional scientists. No prior knowledge is assumed other than a familiarity with chemistry and some basic mathematical concepts.

Table of Contents

PREFACE xi
ACKNOWLEDGEMENTS xv
CHAPTER 1. REPRESENTATION AND MANIPULATION OF 2D MOLECULAR STRUCTURES 1(26)
1. Introduction
1(1)
2. Computer Representations of Chemical Structures
1(7)
2.1 Graph Theoretic Representations of Chemical Structures
2(2)
2.2 Connection Tables and Linear Notations
4(2)
2.3 Canonical Representations of Molecular Structures
6(2)
3. Structure Searching
8(1)
4. Substructure Searching
9(10)
4.1 Screening Methods
11(2)
4.2 Algorithms for Subgraph Isomorphism
13(4)
4.3 Practical Aspects of Structure Searching
17(2)
5. Reaction Databases
19(2)
6. The Representation of Patents and Patent Databases
21(3)
7. Relational Database Systems
24(2)
8. Summary
26(1)
CHAPTER 2. REPRESENTATION AND MANIPULATION OF 3D MOLECULAR STRUCTURES 27(26)
1. Introduction
27(1)
2. Experimental 3D databases
28(3)
3. 3D Pharmacophores
31(2)
4. Implementation of 3D database Searching
33(1)
5. Theoretical 3D Databases
34(6)
5.1 Structure-Generation Programs
34(1)
5.2 Conformational Search and Analysis
35(1)
5.3 Systematic Conformational Search
35(3)
5.4 Random Conformational Search
38(1)
5.5 Other Approaches to Conformational Search
39(1)
5.6 The Generation of Distance Keys for Flexible Molecules
39(1)
6. Methods to Derive 3D Pharmacophores
40(11)
6.1 Pharmacophore Mapping using Constrained Systematic Search
41(2)
6.2 Pharmacophore Mapping using Clique Detection
43(2)
6.3 The Maximum Likelihood Method for Pharmacophore Mapping
45(2)
6.4 Pharmacophore Mapping using a Genetic Algorithm
47(2)
6.5 Practical Aspects of Pharmacophore Mapping
49(2)
7. Applications of 3D Pharmacophore Mapping and 3D Database Searching
51(1)
8. Summary
52(1)
CHAPTER 3. MOLECULAR DESCRIPTORS 53(18)
1. Introduction
53(1)
2. Descriptors Calculated from the 2D Structure
54(11)
2.1 Simple Counts
54(1)
2.2 Physicochemical Properties
54(3)
2.3 Molar Refractivity
57(1)
2.4 Topological Indices
57(2)
2.5 Kappa Shape Indices
59(3)
2.6 Electrotopological State Indices
62(1)
2.7 2D Fingerprints
63(1)
2.8 Atom-Pairs and Topological Torsions
63(1)
2.9 BCUT Descriptors
64(1)
3. Descriptors Based on 3D Representations
65(3)
3.1 3D Fragment Screens
65(1)
3.2 Pharmacophore Keys
66(1)
3.3 Other 3D Descriptors
67(1)
4. Data Verification and Manipulation
68(7)
4.1 Data Spread and Distribution
68(1)
4.2 Scaling
69(1)
4.3 Correlations
69(2)
4.4 Reducing the Dimensionality of a Data Set: Principal Components Analysis
71(4)
5. Summary
75
CHAPTER 4. COMPUTATIONAL MODELS 71(32)
1. Introduction
77(1)
2. Historical Overview
77(2)
3. Deriving a QSAR Equation: Simple and Multiple Linear Regression
79(6)
3.1 The Squared Correlation Coefficient, R2
81(1)
3.2 Cross-Validation
82(1)
3.3 Other Measures of a Regression Equation
83(2)
4. Designing a QSAR "Experiment"
85(6)
4.1 Selecting the Descriptors to Include
86(1)
4.2 Experimental Design
86(2)
4.3 Indicator Variables
88(1)
4.4 Free-Wilson Analysis
89(1)
4.5 Non-Linear Terms in QSAR Equations
89(1)
4.6 Interpretation and Application of a QSAR Equation
90(1)
5. Principal Components Regression
91(1)
6. Partial Least Squares
92(5)
7. Molecular Field Analysis and Partial Least Squares
97(4)
8. Summary
101(2)
CHAPTER 5. SIMILARITY METHODS 103(20)
1. Introduction
103(2)
2. Similarity Based on 2D Fingerprints
105(1)
3. Similarity Coefficients
106(4)
3.1 Properties of Similarity and Distance Coefficients
108(2)
4. Other 2D Descriptor Methods
110(2)
4.1 Maximum Common Subgraph Similarity
110(1)
4.2 Reduced Graph Similarity
111(1)
5. 3D Similarity
112(10)
5.1 Alignment-Independent Methods
113(2)
5.2 Alignment Methods
115(1)
5.3 Field-Based Alignment Methods
115(3)
5.4 Gnomonic Projection Methods
118(1)
5.5 Finding the Optimal Alignment
119(1)
5.6 Comparison and Evaluation of Similarity Methods
119(3)
6. Summary
122(1)
CHAPTER 6. SELECTING DIVERSE SETS OF COMPOUNDS 123(24)
1. Introduction
123(1)
2. Cluster Analysis
124(9)
2.1 Hierarchical Clustering
126(2)
2.2 Selecting the Appropriate Number of Clusters
128(2)
2.3 Non-Hierarchical Clustering
130(1)
2.4 Efficiency and Effectiveness of Clustering Methods
131(2)
3. Dissimilarity-Based selection methods
133(4)
3.1 Efficiency and Effectiveness of DBC S Methods
135(2)
4. Cell-Based Methods
137(5)
4.1 Partitioning Using Pharmacophore Keys
141(1)
5. Optimisation Methods
142(2)
6. Comparison and Evaluation of Selection Methods
144(1)
7. Summary
145(2)
CHAPTER 7. ANALYSIS OF HIGH-THROUGHPUT SCREENING DATA 147(18)
1. Introduction
147(3)
2. Data Visualisation
150(3)
2.1 Non-Linear Mapping
151(2)
3. Data Mining Methods
153(10)
3.1 Substructural Analysis
154(1)
3.2 Discriminant Analysis
155(2)
3.3 Neural Networks
157(3)
3.4 Decision Trees
160(3)
4. Summary
163(2)
CHAPTER 8. VIRTUAL SCREENING 165(24)
1. Introduction
165(2)
2. "Drug-Likeness" and Compound Filters
167(3)
3. Structure-Based Virtual Screening
170(11)
3.1 Protein-Ligand Docking
171(3)
3.2 Scoring Functions for Protein-Ligand Docking
174(5)
3.3 Practical Aspects of Structure-Based Virtual Screening
179(2)
4. The Prediction of ADMET Properties
181(7)
4.1 Hydrogen Bonding Descriptors
182(1)
4.2 Polar Surface Area
183(2)
4.3 Descriptors Based on 3D Fields
185(1)
4.4 Toxicity Prediction
186(2)
5. Summary
188(1)
CHAPTER 9. COMBINATORIAL CHEMISTRY AND LIBRARY DESIGN 189(20)
1. Introduction
189(2)
2. Diverse and Focussed Libraries
191(2)
3. Library Enumeration
193(2)
4. Combinatorial Library Design Strategies
195(2)
4.1 Monomer-Based Selection
195(1)
4.2 Product-Based Selection
196(1)
5. Approaches to Product-Based Library Design
197(3)
6. Multiobjective Library Design
200(3)
6.1 Multiobjective Library Design using a MOLA
201(2)
7. Practical Examples of Library Design
203(4)
7.1 Structure-Based Library Design
203(1)
7.2 Library Design in Lead Optimisation
204(3)
8. Summary
207(2)
APPENDIX 1. MATRICES, EIGENVECTORS AND EIGENVALUES. 209(4)
APPENDIX 2. CONFORMATION, ENERGY CALCULATIONS AND ENERGY SURFACES. 213(6)
FURTHER READING 219(6)
REFERENCES 225(26)
INDEX 251

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