Computer Applications in Pharmaceutical Research and Development (Wiley Series in Drug ...

840 Pages·2006·12.73 MB·English

COMPUTER
APPLICATIONS IN
PHARMACEUTICAL
RESEARCH AND
DEVELOPMENT
SEAN EKINS, M.SC., PH.D., D.SC.
A JOHN WILEY & SONS, INC., PUBLICATION
COMPUTER
APPLICATIONS IN
PHARMACEUTICAL
RESEARCH AND
DEVELOPMENT
WILEY SERIES IN DRUG DISCOVERY
AND DEVELOPMENT
Binghe Wang, Series Editor
Computer Applications in Pharmaceutical Research and Development
Edited by Sean Ekins
COMPUTER
APPLICATIONS IN
PHARMACEUTICAL
RESEARCH AND
DEVELOPMENT
SEAN EKINS, M.SC., PH.D., D.SC.
A JOHN WILEY & SONS, INC., PUBLICATION
Copyright © 2006 by John Wiley & Sons, Inc. All rights reserved
Published by John Wiley & Sons, Inc., Hoboken, New Jersey
Published simultaneously in Canada
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LibraryofCongressCataloging-in-PublicationData:
Computer applications in pharmaceutical research and development / [edited by] Sean Ekins.
p. ; cm.—(Wiley series in drugdiscovery and development)
Includes bibliographical references and index.
ISBN-13: 978-0-471-73779-7 (cloth)
ISBN-10:0-471-73779-8 (cloth)
1. Pharmacy—Data processing. 2. Pharmacology—Data processing. 3. Pharmaceutical
industry—Data processing. I. Ekins,Sean. II. Series.
[DNLM: 1. Drug Industry. 2. Medical Informatics. 3. Drug Approval—methods.
4. DrugEvaluation—methods. 5. Drug Evaluation, Preclinical—methods.
QV 26.5 C7374 2006]
RS122.2.C66 2006
615′.10285—dc22
2005033608
Printed in the United States of America
10 9 8 7 6 5 4 3 2 1
For Rosalynd
Failures are notsomething to be avoided. You want them tohappen as quickly
as you can so you can make progress rapidly
—Gordon Moore

CONTENTS
PREFACE xi
ACKNOWLEDGMENTS xiii
CONTRIBUTORS xv
PARTI: COMPUTERSINPHARMACEUTICALRESEARCH
ANDDEVELOPMENT:AGENERALOVERVIEW 1
1. History of Computersin Pharmaceutical Research and
Development:ANarrative 3
Donald B. Boyd and Max M.Marsh
2. ComputersasDataAnalysisandDataManagementToolsin
PreclinicalDevelopment 51
Weiyong Liand Kenneth Banks
3. Statistical Modeling in Pharmaceutical Research and
Development 67
Andrea de Gaetano, Simona Panunzi, Benoit Beck, and
Bruno Boulanger
PARTII: UNDERSTANDINGDISEASES:MINING
COMPLEXSYSTEMSFORKNOWLEDGE 103
4. DrugDiscovery fromHistoricHerbalTexts 105
Eric J. Buenz
vii
viii CONTENTS
5. ContextualizingtheImpactofBioinformaticsonPreclinical
DrugandVaccineDiscovery 121
Darren R. Flower
6. SystemsApproachesforPharmaceuticalResearchand
Development 139
Sean Ekinsand Craig N. Giroux
PARTIII: SCIENTIFICINFORMATIONHANDLINGAND
ENHANCINGPRODUCTIVITY 167
7. InformationManagement—Biodata inLifeSciences 169
Richard K.Scottand Anthony Parsons
8. Chemoinformatics Techniques for ProcessingChemical
Structure Databases 187
Valerie J. Gillet and Peter Willett
9. Electronic LaboratoryNotebooks 209
Alfred Nehme and Robert A. Scoffi n
10. Strategies forUsingInformationEffectivelyin Early-Stage
DrugDiscovery 229
David J. Wild
11. Improving the Pharmaceutical R&D Process: How
Simulation Can Support Management Decision Making 247
Andrew Chadwick, Jonathan Moore, Maggie A.Z. Hupcey,
and Robin Purshouse
PARTIV: COMPUTERSINDRUGDISCOVERY 275
12. ComputersandProteinCrystallography 277
David J. Edwards and Roderick E. Hubbard
13. Computers,Cheminformatics, and the Medicinal Chemist 301
Weifan Zheng and Michael Jones
14. TheChallengesofMakingUsefulProtein-LigandFree
Energy PredictionsforDrugDiscovery 321
Jun Shimada
15. ComputerAlgorithmsforSelectingMoleculeLibraries
forSynthesis 353
Konstantin V. Balakin, Nikolay P. Savchuk, and Alex Kiselyov
16. Success StoriesofComputer-AidedDesign 377
Hugo Kubinyi