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An Introduction to Computational Biochemistry
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  • Wiley

More About This Title An Introduction to Computational Biochemistry

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This comprehensive text offers a solid introduction to the biochemical principles and skills required for any researcher applying computational tools to practical problems in biochemistry. Each chapter includes an introduction to the topic, a review of the biological concepts involved, a discussion of the programming and applications used, key references, and problem sets and answers. Providing detailed coverage of biochemical structures, enzyme reactions, metabolic simulation, genomic and proteomic analyses, and molecular modeling, this is the perfect resource for students and researchers in biochemistry, bioinformatics, bioengineering and computational science.
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Preface ix

1 INTRODUCTION 1

1.1. Biochemistry: Studies of Life at the Molecular Level 1

1.2. Computer Science and Computational Sciences 5

1.3. Computational Biochemistry: Application of Computer Technology to Biochemistry 6

References 9

2 BIOCHEMICAL DATA: ANALYSIS AND MANAGEMENT 11

2.1. Statistical Analysis of Biochemical Data 11

2.2. Biochemical Data Analysis with Spreadsheet Application 20

2.3. Biochemical Data Management with Database Program 28

2.4. Workshops 31

References 40

3 BIOCHEMICAL EXPLORATION: INTERNET RESOURCES 41

3.1. Introduction to Internet 41

3.2. Internet Resources of Biochemical Interest 46

3.3. Database Retrieval 48

3.4. Workshops 52

References 52

4 MOLECULAR GRAPHICS: VISUALIZATION OF BIOMOLECULES 53

4.1. Introduction to Computer Graphics 53

4.2. Representation of Molecular Structures 56

4.3. Drawing and Display of Molecular Structures 60

4.4. Workshops 69

References 70

5 BIOCHEMICAL COMPOUNDS: STRUCTURE AND ANALYSIS 73

5.1. Survey of Biomolecules 73

5.2. Characterization of Biomolecular Structures 80

5.3. Fitting and Search of Biomolecular Data and Information 87

5.4. Workshops 98

References 103

6 DYNAMIC BIOCHEMISTRY: BIOMOLECULAR INTERACTIONS 107

6.1. Biomacromolecule—Ligand Interactions 107

6.2. Receptor Biochemistry and Signal Transduction 111

6.3. Fitting of Binding Data and Search for Receptor Databases 113

6.4. Workshops 119

References 121

7 DYNAMIC BIOCHEMISTRY: ENZYME KINETICS 123

7.1. Characterization of Enzymes 123

7.2. Kinetics of Enzymatic Reactions 126

7.3. Search and Analysis of Enzyme Data 133

7.4. Workshops 140

References 144

8 DYNAMIC BIOCHEMISTRY: METABOLIC SIMULATION 147

8.1. Introduction to Metabolism 147

8.2. Metabolic Control Analysis 152

8.3. Metabolic Databases and Simulation 153

8.4. Workshops 160

References 162

9 GENOMICS: NUCLEOTIDE SEQUENCES AND RECOMBINANT DNA 165

9.1. Genome, DNA Sequence, and Transmission of Genetic Information 165

9.2. Recombinant DNA Technology 169

9.3. Nucleotide Sequence Analysis 171

9.4. Workshops 179

References 181

10 GENOMICS: GENE IDENTIFICATION 183

10.1. Genome Information and Features 183

10.2. Approaches to Gene Identification 185

10.3. Gene Identification with Internet Resources 188

10.4. Workshops 204

References 207

11 PROTEOMICS: PROTEIN SEQUENCE ANALYSIS 209

11.1. Protein Sequence: Information and Features 209

11.2. Database Search and Sequence Alignment 213

11.3. Proteomic Analysis Using Internet Resources: Sequence and Alignment 221

11.4. Workshops 228

References 230

12 PROTEOMICS: PREDICTION OF PROTEIN STRUCTURES 233

12.1. Prediction of Protein Secondary Structures from Sequences 233

12.2. Protein Folding Problems and Functional Sites 236

12.3. Proteomic Analysis Using Internet Resources: Structure and Function 243

12.4. Workshops 264

References 266

13 PHYLOGENETIC ANALYSIS 269

13.1. Elements of Phylogeny 269

13.2. Methods of Phylogenetic Analysis 271

13.3. Application of Sequence Analyses in Phylogenetic Inference 275

13.4. Workshops 280

References 284

14 MOLECULAR MODELING: MOLECULAR MECHANICS 285

14.1. Introduction to Molecular Modeling 285

14.2. Energy Minimization, Dynamics Simulation, and Conformational Search 287

14.3. Computational Application of Molecular Modeling Packages 296

14.4. Workshops 311

References 313

15 MOLECULAR MODELING: PROTEIN MODELING 315

15.1. Structure Similarity and Overlap 315

15.2. Structure Prediction and Molecular Docking 319

15.3. Applications of Protein Modeling 322

15.4. Workshops 337

References 340

APPENDIX 343

1. List of Software Programs 343

2. List of World Wide Web Servers 345

3. Abbreviations 353

INDEX 357

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English

"…for any faculty members trying to introduce or expand the computational element of their courses, this book should provide some useful ideas and student exercises.” (Biochemistry and Molecular Education, Jan/Feb 2003)

"...a worthwhile addition to a personal bookshelf or an institution's library..." (Journal of Chemical Education, January 2003)

"...each chapter is a treasure chest of databases, software, and opportunities...a worthwile addition to a personal bookshelf or an institution’s library..." (Journal of Chemical Education, Vol. 80, No. 1, January 2003)

"...provides an excellent introduction to this newly established discipline...recommendable and a worthy investment for students..." (ChemBioChem, 2003)

"...an excellent introduction to this newly established discipline...recommendable and a worthy investment for students..." (ChemBioChem, Vol 4(4), 2003)

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