BIOINFORMATICS:
A REVOLUTION IN DRUG DISCOVERY
Written by the Head of Advanced Technology and Informatics at one of the world's top pharmaceutical
companies, this report is a guide to the very latest bioinformatics strategies. Bioinformatics shortens the
time to candidate selection by harnessing the latest information technology methods.
This report will enable you to assess this fast-moving area and to implement an effective bioinformatics strategy.
It helps you to understand exactly what bioinformatics is; assess the benefits of investing in bioinformatics; analyse
the impact that bioinformatics has upon drug discovery and access information on the platforms, tools and providers
available.
CONTENTS
LIST OF FIGURES
EXECUTIVE SUMMARY
ABBREVIATIONS AND GLOSSARY
CHAPTER 1 INTRODUCTION
1.1 What is bioinformatics?
1.2 Tools
1.2.1 Entrez
1.2.2 Sequence Retrieval System
1.2.3 The Atlas of Protein and Genomic Sequences
1.2.4 Protein Extraction Description and Analysis Tool
1.2.5 Basic Local Alignment Search Tool
1.2.6 FASTA
1.2.7 BLITZ
1.2.8 GRAIL
1.2.9 The Staden Package
1.2.10 A Caenorhabditis elegans database
1.2.11 RasMol
1.2.12 European Molecular Biology Open Software Suite
1.3 Platforms
1.3.1 Application programming interfaces
1.3.2 Bioinformatics operating systems and platforms
1.3.3 Application Frameworks
1.4 Providers
1.4.1 The National Center for Biotechnology Information
1.4.2 The European Bioinformatics Institute
1.4.3 The European Molecular Biology Network
1.4.4 The Centre for Information Biology
1.4.5 The National Centre for Genome Resources
1.4.6 The Protein Identification Resource
1.4.7 The Munich Information Centre for Protein Sequences
1.4.8 The UK Human Genome Mapping Project Resource Centre
1.4.9 SEQNET
1.5 Intranets and Extranets
1.6 Public domain databases
1.6.1 The Genome Database
1.6.2 Online Mendelian Inheritance in Man
1.6.3 The International Nucleic Acid Sequence Database
1.6.3.1 Features of the INSD
1.6.4 The Genome Sequence Database
1.6.5 The Merck Gene Index
1.6.6 Other nucleic acid sequence databases
1.6.7 Protein sequence databanks
1.6.8 PIR-International
1.6.9 SWISS-PROT
1.6.10 Protein Data Bank
1.6.11 Protein sequence motif databases
1.6.12 PROSITE: a dictionary of protein sites and patterns
1.6.13 PRINTS
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CHAPTER 2 BENEFITS OF BIOINFORMATICS IN DRUG DISCOVERY
2.1 Impact on strategies for drug candidate selection
2.2 Exploratory investigations
2.3 Alerting systems
2.4 Model building
2.5 Target identification and validation
2.6 Lead generation
2.7 Lead optimisation
2.8 Candidate selection
2.9 Development
2.10 Cost versus benefit
2.11 Genetics
2.12 Improving decision making
2.13 Increasing throughput
2.14 Issues and risks
2.14.1 Industry consolidation
2.14.2 Quantity of data
2.14.3 In silico biology
CHAPTER 3 DESIGNING AN EFFECTIVE BIOINFORMATICS STRATEGY
3.1 Designing bioinformatics strategies with the Applications Portfolio Model
3.1.1 High Potential
3.1.2 Strategic
3.1.3 Key Operational
3.1.4 Support
3.2 Rapid prototyping
3.3 Object-orientation
3.4 Which provider/which product?
3.5 Electronic access to the published literature
3.6 Integration of new products into existing systems
3.7 Maximising security of information
CHAPTER 4 CASE STUDIES
4.1 What bioinformatics strategies are the key players adopting?
4.2 Bioinformatics for molecular biology
4.2.1 Bioinformatics for utilising ESTs
4.2.2 Bioinformatics for genetics
4.3 Which pharmaceutical companies are dealing with which bioinformatics providers?
4.3.1 Merck KGaA
4.3.2 Pfizer
4.3.3 Zeneca
4.3.4 SmithKline Beecham
4.3.4.1 In silico gene cloning
4.3.4.2 Sequence homology driven target identification
4.3.4.3 Expression profiling of transcript patterns
4.3.4.4 New G-protein coupled receptors
4.3.4.5 Positional cloning
4.3.4.6 Gene Informatics at SB
4.3.5 Novartis
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CHAPTER 5 THE FUTURE
5.1 New opportunities for scientific software development
5.2 Bioinformatics as an opportunity for generating competitive advantage
5.3 Large-scale sequencing
5.4 Virtual bioinformatics companies
5.5 The 'rat'
5.6 Simulation and modelling
CHAPTER 6 COMPANY PROFILES
6.1 First generation bioinformatics companies
6.1.1 DNA* (DNASTAR)
6.1.2 Informax Inc
6.1.3 Genetics Computer Group
6.2 Pharmaceutical company software houses
6.2.1 MDL Information Systems Inc
6.2.2 Molecular Simulations Inc
6.2.3 Oxford Molecular Group
6.3 Genomics companies
6.3.1 LION Bioscience AG
6.3.2 Incyte Pharmaceuticals Inc
6.3.3 Human Genome Sciences
6.3.4 CuraGen
6.4 'New wave' bioinformatics companies
6.4.1 NetGenics
6.4.2 Pangea Systems
6.4.3 Genomica
6.4.4 Molecular Applications Group
PUBLISHED: OCTOBER 1998
REF: BS973E
PAGES: 113
PRICE: £143/$300/¥35,000