Bioinformatics - from genomes to therapies

Cover......Page 1
Frontmatter......Page 2
Contents......Page 9
Preface......Page 57
List of Contributors......Page 60
1 Bioinformatics -- From Genomes to Therapies......Page 69
2 Bioinformatics Support for Genome-Sequencing Projects......Page 93
3 Sequence Alignment and Sequence Database Search......Page 124
4 Phylogeny Reconstruction......Page 150
5 Finding Protein-coding Genes......Page 196
6 Analyzing Regulatory Regions in Genomes......Page 226
7 Finding Repeats in Genome Sequences......Page 263
8 Analyzing Genome Rearrangements......Page 300
9 Predicting Simplified Features of Protein Structure......Page 326
10 Homology Modeling in Biology and Medicine......Page 361
11 Protein Fold Recognition Based on Distant Homologs......Page 414
12 De Novo Structure Prediction: Methods and Applications......Page 452
13 Structural Genomics......Page 482
14 RNA Secondary Structures......Page 502
15 RNA Tertiary Structure Prediction......Page 553
16 Docking and Scoring for Structure-based Drug Design......Page 602
17 Modeling Protein–Protein and Protein–DNA Docking......Page 661
18 Lead Identification by Virtual Screening......Page 711
19 Efficient Strategies for Lead Optimization by Simultaneously Addressing Affinity, Selectivity and Pharmacokinetic Parameters......Page 765
20 Modeling and Simulating Metabolic Networks......Page 815
21 Inferring Gene Regulatory Networks......Page 866
22 Modeling Cell Signaling Networks......Page 887
23 Dynamics of Virus–Host Cell Interaction......Page 919
24 DNA Microarray Technology and Applications – An Overview......Page 957
25 Low-level Analysis of Microarray Experiments......Page 987
26 Classification of Patients......Page 1015
27 Classification of Genes......Page 1050
28 Proteomics: Beyond cDNA......Page 1079
29 Ontologies for Molecular Biology......Page 1116
30 Inferring Protein Function from Sequence......Page 1142
31 Analyzing Protein Interaction Networks......Page 1175
32 Inferring Protein Function from Genomic Context......Page 1232
33 Inferring Protein Function from Protein Structure......Page 1264
34 Mining Information on Protein Function from Text......Page 1306
35 Integrating Information for Protein Function Prediction......Page 1349
36 The Molecular Basis of Predicting Druggability......Page 1367
37 Comparative Genomics......Page 1387
38 Association Studies of Complex Diseases......Page 1427
Appendix A......Page 1475
39 Pharmacogenetics/Pharmacogenomics......Page 1479
40 Evolution of Drug Resistance in HIV......Page 1508
41 Analyzing the Evolution of Infectious Bacteria......Page 1547
42 Integrating Biological Databases......Page 1575
43 Visualization of Biological Data......Page 1622
44 Using Distributed Data and Tools in Bioinformatics Applications......Page 1676
45 Future Trends......Page 1700
Index......Page 1736
Name Index......Page 1776