Practical Bioinformatics (eBook)

Janusz M. Bujnicki (Autor)

eBook Download: PDF

2008 | 1. Auflage
XVII, 266 Seiten
Springer-Verlag
978-3-540-74268-5 (ISBN)

Infos

"The book is unique in that it bridges the gap between bioinformaticists and molecular biologists, i.e. the developers and the users of computational methods for biological data analysis and in that it presents examples of practical applications of the bioinformatics tools in the ""daily practice"" of an experimental research scientist. The book starts with reviews on computational methods for protein sequence-structure-function analysis (sequence studies, structure prediction), followed by methods that explicitly utilize experimental data routinely obtained in the laboratory to improve the functional predictions. The second part comprises a series of examples on how particular applications of different types of bioinformatics methods in combination with experimental studies to validate the hypotheses have led to important scientific discoveries. Therefore, the book is a guide to application of bioinformatics methods in molecular biology, addressed mainly to the research scientists, postdocs, and advanced graduate students."

Inhalt

Preface 5
Contents 7
Contributors 14
Computational Methods for Protein Structure Prediction and Fold Recognition 17
1 Primary Structure Analysis 17
2 Secondary Structure Prediction 21
3 Protein Fold-Recognition 24
4 Predicting All-in-One-Go 28
5 Pitfalls of Fold Recognition 30
References 32
‘Meta’Approaches to Protein Structure Prediction 38
1 Introduction 38
2 The Utility of Servers as Standard Tools for Protein Structure Prediction 39
3 Future Prospects 46
References 47
From Molecular Modeling to Drug Design 50
1 Introduction 50
2 Comparative Modeling 53
3 Model-Based Drug Design 67
4 Conclusions 77
References 78
Structure Determination of Macromolecular Complexes by Experiment and Computation 87
1 Introduction 87
2 Hybrid Approaches to Determination of Assembly Structures 91
3 Comparative Modeling for Structure Determination of Macromolecular Complexes 96
4 Conclusions 105
References 106
Modeling Protein Folding Pathways 111
1 Introduction: Darwin Versus Boltzmann 111
2 Knowledge-Based Models for Folding Pathways 113
3 ROSETTA: Folding Simulations Using a Fragment Library 115
4 HMMSTR-CM: Folding Pathways Using Contact Maps 120
5 Conclusions 132
References 132
Structural Bioinformatics and NMR Structure Determination 137
1 Introduction: NMR and Structural Bioinformatics 137
2 Algorithms for NMR Structure Calculation 138
3 Internal Dynamics and NMR Structure Determination 141
4 Structure Validation 142
5 Structural Genomics by NMR 143
6 Databanks and Databases 146
7 Conclusions 147
References 148
Bioinformatics-Guided Identification and Experimental Characterization of Novel RNA Methyltransferases 152
1 Introduction 152
2 Traditional and Novel Approaches to Identification of New RNA- Modification Enzymes 158
3 Bioinformatics: Terminology, Methodology, and Applications to RNA MTases 159
4 Conclusions 173
References 175
Finding Missing tRNA Modification Genes: a Comparative Genomics Goldmine 182
1 Missing tRNA Modification Genes 182
2 Comparative Genomics: an Emerging Tool to Identify Missing Genes 186
3 Finding Genes for Simple tRNA Modifications 188
4 Finding Complex Modification Pathway Genes 191
5 Conclusions 196
References 197
Evolution and Function of Processosome, the Complex that Assembles Ribosomes in Eukaryotes: Clues from Comparative Sequence Analysis 204
1 Introduction 204
2 Sequence Analysis of the Processosome Components 205
3 Phyletic Patterns 225
4 Concluding remarks 229
References 230
Bioinformatics-Guided Experimental Characterization of Mismatch- Repair Enzymes and Their Relatives 233
1 Introduction 233
2 Sau3AI – Similar Folds for N- and C-Terminal Domains 237
3 Identification of the Methylation Sensor of MutH 244
A 248
B 248
C 248
4 Conclusions 250
References 251
Predicting Functional Residues in DNA Glycosylases by Analysis of Structure and Conservation 254
1 Introduction 254
2 Generating Predictions: Sequence Selection and Analysis 255
3 Testing the Predictions: Mutational Analysis of Residues Defining Substrate Specificity in Formamidopyrimidine- DNA Glycosylase 262
4 Refining the Predictions: Analysis of Substrate Specificity in the Endonuclease III Family 265
References 270
Subject Index 273

Produkt-Details

• Erscheint lt. Verlag: 1.1.2008
• Sprache: englisch
• Themenwelt: Studium ► 1. Studienabschnitt (Vorklinik) ► Biochemie / Molekularbiologie
• Themenwelt: Naturwissenschaften ► Biologie ► Genetik / Molekularbiologie
• Schlagworte: Bioinformatics • conservation • DNA • drug design • enzymes • eukaryote • Eukaryotes • Evolution • Genome • genomics • Protein • Protein function analysis • Protein sequence analysis • protein structure analysis • RNA • Sequence Analysis • termination • tRNA
• ISBN-10: 3-540-74268-9 / 3540742689
• ISBN-13: 978-3-540-74268-5 / 9783540742685