Catalogue


Computational drug design [electronic resource] : a guide for computational and medicinal chemists /
David C. Young.
imprint
Hoboken, N.J. : John Wiley & Sons, c2009.
description
xxxvi, 307 p. : ill. ; 25 cm. + 1 CD-ROM (4 3/4 in.)
ISBN
047012685X (cloth/CD), 9780470126851 (cloth/CD)
format(s)
Book
More Details
imprint
Hoboken, N.J. : John Wiley & Sons, c2009.
isbn
047012685X (cloth/CD)
9780470126851 (cloth/CD)
restrictions
Licensed for access by U. of T. users.
catalogue key
7877082
 
Includes bibliographical references and index.
A Look Inside
About the Author
Author Affiliation
David C. Young, PhD, is HPC Computational Specialist for Computer Sciences Corp., under contract to the Alabama Supercomputer Authority, where he heads user and application support for research and educational activities. Dr. Young has extensive experience in designing drugs and writing drug design software. He is the author of Computational Chemistry: A Practical Guide for Applying Techniques to Real World Problems, also published by Wiley.
Reviews
Review Quotes
"As the author states, 'this book is very industry-centric' and was designed to explore the drug design process through the computational techniques that are used in a typical pharmaceutical industry." (JACS Book Reviews, June 2009)
"In conclusion, this book provides a comprehensive introduction to computational drug design for scientists (e.g. medicinal chemists and pharmacologists, particularly at industrial level) who are not familiar with computational methods and who wish to discuss simulation outcomes with colleagues from computational departments. It provides a similarly comprehensive introduction for students, while also covering aspects not usually touched on by other computational textbooks. Students will then need to deepen their mathematical and theoretical background to become robust computational drug designers." (ChemMedChem, 2010) "The book has been written in very lucid and readable language." (Journal of Medicinal Chemistry, August 2009)"As the author states, 'this book is very industry-centric' and was designed to explore the drug design process through the computational techniques that are used in a typical pharmaceutical industry." (JACS Book Reviews, June 2009)
'The book has been written in very lucid and readable language.' (Journal of Medicinal Chemistry, August 2009)?As the author states, ?this book is very industry-centric? and was designed to explore the drug design process through the computational techniques that are used in a typical pharmaceutical industry.' (JACS Book Reviews, June 2009)
To find out how to look for other reviews, please see our guides to finding book reviews in the Sciences or Social Sciences and Humanities.
Summaries
Main Description
Computational Drug Design covers all of the major computational drug design techniques in use today, focusing on the process that pharmaceutical chemists employ to design a new drug molecule. The discussions of which computational tools to use and when and how to use them are all based on typical pharmaceutical industry drug design processes. Following an introduction, the book is divided into three parts: Part One, The Drug Design Process, sets forth a variety of design processes suitable for a number of different drug development scenarios and drug targets. The author demonstrates how computational techniques are typically used during the design process, helping readers choose the best computational tools to meet their goals. Part Two, Computational Tools and Techniques, offers a series of chapters, each one dedicated to a single computational technique. Readers discover the strengths and weaknesses of each technique. Moreover, the book tabulates comparative accuracy studies, giving readers an unbiased comparison of all the available techniques. Part Three, Related Topics, addresses new, emerging, and complementary technologies, including bioinformatics, simulations at the Cellular and organ level, synthesis route prediction, proteomics, and prodrug approaches. The book's accompanying CD-ROM, a special feature, offers graphics of the molecular structures and dynamic reactions discussed in the book as well as demos from computational drug design software companies. Computational Drug Design is ideal for both students and professionals in drug design, helping them choose and take full advantage of the best computational tools available. Book jacket.
Main Description
Helps you choose the right computational tools and techniques to meet your drug design goalsComputational Drug Design covers all of the major computational drug design techniques in use today, focusing on the process that pharmaceutical chemists employ to design a new drug molecule. The discussions of which computational tools to use and when and how to use them are all based on typical pharmaceutical industry drug design processes.Following an introduction, the book is divided into three parts:Part One, The Drug Design Process, sets forth a variety of design processes suitable for a number of different drug development scenarios and drug targets. The author demonstrates how computational techniques are typically used during the design process, helping readers choose the best computational tools to meet their goals.Part Two, Computational Tools and Techniques, offers a series of chapters, each one dedicated to a single computational technique. Readers discover the strengths and weaknesses of each technique. Moreover, the book tabulates comparative accuracy studies, giving readers an unbiased comparison of all the available techniques.Part Three, Related Topics, addresses new, emerging, and complementary technologies, including bioinformatics, simulations at the cellular and organ level, synthesis route prediction, proteomics, and prodrug approaches.The book's accompanying CD-ROM, a special feature, offers graphics of the molecular structures and dynamic reactions discussed in the book as well as demos from computational drug design software companies.Computational Drug Design is ideal for both students and professionals in drug design, helping them choose and take full advantage of the best computational tools available.
Main Description
Helps you choose the right computational tools and techniques to meet your drug design goals Computational Drug Design covers all of the major computational drug design techniques in use today, focusing on the process that pharmaceutical chemists employ to design a new drug molecule. The discussions of which computational tools to use and when and how to use them are all based on typical pharmaceutical industry drug design processes. Following an introduction, the book is divided into three parts: Part One, The Drug Design Process, sets forth a variety of design processes suitable for a number of different drug development scenarios and drug targets. The author demonstrates how computational techniques are typically used during the design process, helping readers choose the best computational tools to meet their goals. Part Two, Computational Tools and Techniques, offers a series of chapters, each one dedicated to a single computational technique. Readers discover the strengths and weaknesses of each technique. Moreover, the book tabulates comparative accuracy studies, giving readers an unbiased comparison of all the available techniques. Part Three, Related Topics, addresses new, emerging, and complementary technologies, including bioinformatics, simulations at the cellular and organ level, synthesis route prediction, proteomics, and prodrug approaches. The book's accompanying CD-ROM, a special feature, offers graphics of the molecular structures and dynamic reactions discussed in the book as well as demos from computational drug design software companies. Computational Drug Design is ideal for both students and professionals in drug design, helping them choose and take full advantage of the best computational tools available. Note: CD-ROM/DVD and other supplementary materials are not included as part of eBook file.
Main Description
There has been a great surge in the usage of computational drug design techniques over the past 20 years. Filling the need for an easily understood, nonmathematical text on drug design, Computational Drug Design explores the wide range of computational techniques available for the drug design process, and puts them in the framework of the drug design process. This valuable learning source provides students, computational chemists, organic, medicinal and pharmaceutical chemists, and biochemists with a solid perspective on the entire breadth of the field.
Table of Contents
Prefacep. xv
Acknowledgmentsp. xix
About the Authorp. xxi
Symbols Used in This Bookp. xxiii
Book Abstractp. xxix
Introductionp. 1
A Difficult Problemp. 1
An Expensive Problemp. 2
Where Computational Techniques are Usedp. 3
Bibliographyp. 5
The Drug Design Processp. 7
Properties that Make a Molecule a Good Drugp. 9
Compound Testingp. 10
Biochemical Assaysp. 11
Cell-Based Assaysp. 13
Animal Testingp. 14
Human Clinical Trialsp. 15
Molecular Structurep. 16
Activityp. 16
Bioavailability and Toxicityp. 24
Drug Side Effectsp. 26
Multiple Drug Interactionsp. 26
Metrics for Drug-Likenessp. 27
Exceptions to the Rulesp. 33
Bibliographyp. 35
Target Identificationp. 41
Primary Sequence and Metabolic Pathwayp. 41
Crystallographyp. 43
2D NMRp. 44
Homology Modelsp. 45
Protein Foldingp. 45
Bibliographyp. 46
Target Characterizationp. 47
Analysis of Target Mechanismp. 47
Kinetics and Crystallographyp. 48
Automated Crevice Detectionp. 48
Transition Structures and Reaction Coordinatesp. 49
Molecular Dynamics Simulationsp. 49
Where the Target is Expressedp. 50
Pharmacophore Identificationp. 50
Choosing an Inhibitor Mechanismp. 51
Bibliographyp. 52
The Drug Design Process for a Known Protein Targetp. 53
The Structure-Based Design Processp. 53
Initial Hitsp. 55
Compound Refinementp. 56
ADMETp. 67
Drug Resistancep. 67
Bibliographyp. 68
The Drug Design Process for an Unknown Targetp. 71
The Ligand-Based Design Processp. 71
Initial Hitsp. 72
Compound Refinementp. 73
ADMETp. 74
Bibliographyp. 74
Drug Design for Other Targetsp. 75
DNA Bindingp. 76
RNA as a Targetp. 78
Allosteric Sitesp. 79
Receptor Targetsp. 80
Steroidsp. 81
Targets inside Cellsp. 82
Targets within the Central Nervous Systemp. 83
Irreversibly Binding Inhibitorsp. 84
Upregulating Target Activityp. 84
Bibliographyp. 85
Compound Library Designp. 87
Targeted Libraries versus Diverse Librariesp. 87
From Fragments versus from Reactionsp. 89
Non-Enumerative Techniquesp. 90
Drug-Likeness and Synthetic Accessibilityp. 91
Analyzing Chemical Diversity and Spanning known Chemistriesp. 93
Compound Selection Techniquesp. 96
p. 99
Computational Tools and Techniquesp. 103
Homology Model Buildingp. 105
How much Similarity is Enough?p. 106
Steps for Building a Homology Modelp. 107
Step 1: Template Identificationp. 108
Step 2: Alignment between the Unknown and the Templatep. 108
Step 3: Manual Adjustments to the Alignmentp. 110
Step 4: Replace Template Side Chains with Model Side Chainsp. 111
Step 5: Adjust Model for Insertions and Deletionsp. 111
Step 6: Optimization of the Modelp. 112
Step 7: Model Validationp. 112
Step 8: If Errors are Found, Iterate Back to Previous Stepsp. 115
Reliability of Resultsp. 116
Bibliographyp. 117
Molecular Mechanicsp. 119
A Really Brief Introduction to Molecular Mechanicsp. 119
Force Fields for Drug Designp. 121
Bibliographyp. 123
Protein Foldingp. 125
The Difficulty of the Problemp. 125
Algorithmsp. 127
Reliability of Resultsp. 129
Conformational Analysisp. 130
Bibliographyp. 131
Dockingp. 133
Introductionp. 133
Search Algorithmsp. 135
Searching the Entire Spacep. 135
Grid Potentials versus Full Force Fieldp. 137
Flexible Active Sitesp. 138
Ligands Covalently Bound to the Active Sitep. 138
Hierarchical Docking Algorithmsp. 139
Scoringp. 141
Energy Expressions and Consensus Scoringp. 141
Binding Free Energiesp. 141
Solvationp. 144
Ligands Covalently Bound to the Active Sitep. 144
Metrics for Goodness of Fitp. 144
Validation of Resultsp. 145
Comparison of Existing Search and Scoring Methodsp. 146
Special Systemsp. 153
The Docking Processp. 155
Protein Preparationp. 156
Building the Ligandp. 156
Setting the Bounding Boxp. 157
Docking Optionsp. 157
Running the Docking Calculationp. 158
Analysis of Resultsp. 158
Bibliographyp. 159
Pharmacophore Modelsp. 161
Components of a Pharmacophore Modelp. 163
Creating a Pharmacophore Model from Active Compoundsp. 164
Creating a Pharmacophore Model from the Active Sitep. 166
Searching Compound Databasesp. 167
Reliability of Resultsp. 168
Bibliographyp. 169
QSARp. 171
Conventional QSAR versus 3D-QSARp. 171
The QSAR Processp. 172
Descriptorsp. 175
Automated QSAR Programsp. 176
QSAR versus Other Fitting Methodsp. 177
Bibliographyp. 178
3D-QSARp. 181
The 3D-QSAR Processp. 182
3D-QSAR Software Packagesp. 184
Summaryp. 184
Bibliographyp. 184
Quantum Mechanics in Drug Designp. 187
Quantum Mechanics Algorithms and Softwarep. 188
Modeling Systems with Metal Atomsp. 191
Increased Accuracyp. 191
Computing Reaction Pathsp. 193
Computing Spectrap. 193
Bibliographyp. 194
De novo and Other AI Techniquesp. 197
De novo Building of Compoundsp. 198
Nonquantitative Predictionsp. 201
Quantitative Predictionsp. 203
Bibliographyp. 205
Cheminformaticsp. 207
Smiles, SLN, and Other Chemical Structure Representationsp. 208
Similarity and Substructure Searchingp. 209
2D-to-3D Structure Generationp. 213
Clustering Algorithmsp. 214
Screening Results Analysisp. 217
Database Systemsp. 222
Bibliographyp. 223
Admetp. 225
Oral Bioavailabilityp. 227
Drug Half-Life in the Bloodstreamp. 229
Blood-Brain Barrier Permeabilityp. 231
Toxicityp. 231
Bibliographyp. 234
Multiobjective Optimizationp. 237
Bibliographyp. 240
Automation of Tasksp. 241
Built-In Automation Capabilitiesp. 241
Automation Using External Utilitiesp. 243
Bibliographyp. 244
Related Topicsp. 245
Bioinformaticsp. 247
Bibliographyp. 251
Simulations at the Cellular and Organ Levelp. 253
Cellular Simulationsp. 253
Organ Simulationsp. 256
p. 256
Synthesis Route Predictionp. 259
Bibliographyp. 262
Proteomicsp. 263
p. 264
Prodrug Approachesp. 267
Bibliographyp. 270
Future Developments in Drug Designp. 273
Individual Patient Genome Sequencingp. 273
Analysis of the Entire Proteomep. 274
Drugs Customized for Ethnic Group or Individual Patientp. 274
Genetic Manipulationp. 275
Cloningp. 276
Stem Cellsp. 277
Longevityp. 278
Bibliographyp. 279
About the CDp. 281
Glossaryp. 285
Indexp. 301
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