Chemoinformatics

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Format: Hardcover
Pub. Date: 2006-12-15
Publisher(s): Springer Verlag
List Price: $237.68

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Summary

Chemoinformatics: Theory, Practice & Products covers theory, commercially available packages and applications of Chemoinformatics. Chemoinformatics is broadly defined as the use of information technology to assist in the acquisition, analysis and management of data and information relating to chemical compounds and their properties. This ranges from molecular modelling, to reactions, to spectra, to structure-activity relationships associated with chemicals. Computational scientists, chemists, and biologists all rely on the rapidly evolving field of Chemoinformatics. Chemoinformatics: Theory, Practice & Products is an essential handbook for determining the right Chemoinformatics method or technology to use. There has been an explosion of new Chemoinformatics tools and techniques. Each technique has its own utility, scope, and limitations, as well as meeting resistance to use by experimentalists. The purpose of Chemoinformatics: Theory, Practice & Products is to provide computational scientists, medicinal chemists and biologists with unique practical information and the underlying theories relating to modern Chemoinformatics and related drug discovery informatics technologies. The book also provides a summary of currently available, state-of-the-art, commercial Chemoinformatics products, with a specific focus on databases, toolkits, and modelling technologies designed for drug discovery. It will be broadly useful as a reference text for experimentalists wishing to rapidly navigate the expanding field, as well as the more expert computational scientists wishing to stay up to date. It is primarily intended for applied researchers from the chemical and pharmaceutical industry, academic investigators, and graduate students.

Table of Contents

Forewordp. ix
Chemoinformatics Theoryp. 1
Chemoinformatics - What is it?p. 1
Chemo-versus Bio-informaticsp. 2
Scientific Originsp. 4
Fundamental Conceptsp. 4
Molecular descriptors and chemical spacesp. 4
Chemical spaces and molecular similarityp. 7
Molecular similarity, dissimilarity, and diversityp. 8
Modification and simplification of chemical spacesp. 9
Compound Classification and Selectionp. 11
Cluster analysisp. 12
Partitioningp. 13
Support vector machinesp. 16
Similarity Searchingp. 17
Structural queries and graphsp. 17
Pharmacophoresp. 18
Fingerprintsp. 21
Machine Learning Methodsp. 23
Genetic algorithmsp. 23
Neural networksp. 24
Library Designp. 26
Diverse librariesp. 27
Diversity estimationp. 28
Multi-objective designp. 29
Focused librariesp. 29
Quantitative Structure-Activity Relationship Analysisp. 31
Model buildingp. 31
Model evaluationp. 32
3D-QSARp. 33
4D-QSARp. 34
Probabilistic methodsp. 35
Virtual Screening and Compound Filteringp. 35
Biologically active compoundsp. 35
Virtual and high-throughput screeningp. 36
Filter functionsp. 38
From Theory to Practicep. 40
Database designp. 40
Compound selection for medicinal chemistryp. 42
Computational hit identificationp. 45
Referencesp. 47
Practice and Productsp. 51
Accelrysp. 51
ACD Labsp. 59
Barnard Chemical Information Ltdp. 67
BioBytep. 69
Cambridge Softp. 73
CAS/Scifinderp. 80
ChemAxonp. 87
Chemical Computing Groupp. 98
ChemInnovation Softwarep. 103
ChemNavigatorp. 109
Chimera-Dock-Zinc from UCSFp. 112
Collaborative Drug Discovery (CDD, Inc.)p. 115
Daylightp. 123
Eidogen-Sertanty (previously Libraria)p. 127
Fujitsu Biosciences Group (previously Cache)p. 137
Genegop. 140
GVK-Biop. 144
Hypercubep. 148
IDBSp. 152
Infochemp. 156
Jubilant Biosysp. 164
Leadscopep. 169
MDLp. 171
Milano Chemometrics and QSAR Research Groupp. 180
Molecular Discoveryp. 184
Molecular Networksp. 187
Open Eye Scientific Softwarep. 194
Planaria-Softwarep. 202
PubChemp. 203
PyMolp. 208
RasMol and Protein Explorerp. 211
Schrodinger, LLCp. 215
Scinova Technologiesp. 223
Scitegicp. 226
Simulation Plus, Inc.p. 229
Spotfirep. 236
Summit PKp. 239
Symyxp. 243
TimTecp. 254
Triposp. 259
Subject Appendices
Drug Discovery Informatics Registration Systems and Underlying Toolkits (Appendices 1 and 2)
Drug, Molecular Registration Systems, and Chemistry Data Cartridgesp. 271
Chemoinformatics Toolkits to Develop Applicationsp. 272
Content Databases (Appendices 3-7)
Compound Availability Databasesp. 273
SAR Databasep. 273
Chemical Reaction Databasesp. 274
Patent Databasesp. 275
Other Compound and Drug Databasesp. 275
Drug, Molecule, and Protein Visualization (Appendices 8-10)
Chemical Drawing, Structure Viewing and Modeling Packagesp. 276
Data Analysis and Mining Toolsp. 276
Small Molecule - Protein Visualization Toolsp. 277
Modeling and Algorithms (Appendices 11-17)
Molecular Descriptorsp. 278
Clogp, Tpsa, and Lipinski Property Calculation Systemsp. 279
Qsar/Pharmacophore Programsp. 279
Docking and Crystallographic Softwarep. 280
Quantum Mechanics Calculationsp. 280
PK/ADME/Tox Databases and Predictorsp. 280
Multi-parameter Drug Development/Identification Softwarep. 281
Indexp. 283
Table of Contents provided by Ingram. All Rights Reserved.

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