Structural Bioinformatics

by Gu, Jenny; Bourne, Philip E.

• ISBN13: 9780470181058
• ISBN10: 0470181052
• Edition: 2nd
• Format: Hardcover
• Copyright: 2009-03-16
• Publisher: Wiley-Blackwell

Summary

Structural Bioinformatics was the first major effort to show the application of the principles and basic knowledge of the larger field of bioinformatics to questions focusing on macromolecular structure, such as the prediction of protein structure and how proteins carry out cellular functions, and how the application of bioinformatics to these life science issues can improve healthcare by accelerating drug discovery and development. Designed primarily as a reference, the first edition nevertheless saw widespread use as a textbook in graduate and undergraduate university courses dealing with the theories and associated algorithms, resources, and tools used in the analysis, prediction, and theoretical underpinnings of DNA, RNA, and proteins.This new edition contains not only thorough updates of the advances in structural bioinformatics since publication of the first edition, but also features eleven new chapters dealing with frontier areas of high scientific impact, including: sampling and search techniques; use of mass spectrometry; genome functional annotation; and much more.Offering detailed coverage for practitioners while remaining accessible to the novice, Structural Bioinformatics, Second Edition is a valuable resource and an excellent textbook for a range of readers in the bioinformatics and advanced biology fields.Praise for the previous edition:"This book is a gold mine of fundamental and practical information in an area not previously well represented in book form." Biochemistry and Molecular Education"... destined to become a classic reference work for workers at all levels in structural bioinformatics....recommended with great enthusiasm for educators, researchers, and graduate students." BAMBED"...a useful and timely summary of a rapidly expanding field." Nature Structural Biology"...a terrific job in this timely creation of a compilation of articles that appropriately addresses this issue." Briefings in Bioinformatics

Author Biography

Jenny Gu, PhD, is Assistant Professor at the Skaggs School of Pharmacy and Pharmaceutical Sciences University of California, San Diego. This is her first book.

Philip E. Bourne, PhD, is professor in the Department of Pharmacology at the University of California, San Diego, and Director of Integrated Biosciences at the San Diego Supercomputer Center. He is past president of the International Society for Computational Biology (ISCB). He is author of over 125 peer-reviewed scientific papers and four previous books.

Table of Contents

Foreword	p. xi
Preface	p. xv
Acknowledgments	p. xix
Contributors	p. xxi
Data Collection, Analysis, and Visualization	p. 1
Defining Bioinformatics and Structural Bioinformatics	p. 3
Fundamentals of Protein Structure	p. 15
Fundamentals of DNA and RNA Structure	p. 41
Computational Aspects of High-Throughput Crystallographic Macromolecular Structure Determination	p. 77
Macromolecular Structure Determination by NMR Spectroscopy	p. 93
Electron Microscopy in the Context of Structural Systems Biology	p. 143
Study of Protein Three-Dimensional Structure and Dynamics Using Peptide Amide Hydrogen/Deuterium Exchange Mass Spectrometry (DXMS) and Chemical Cross-Linking with Mass Spectrometry to Constrain Molecular Modeling	p. 171
Search and Sampling in Structural Bioinformatics	p. 207
Molecular Visualization	p. 237
Data Representation and Databases	p. 269
The PDB Format, mmCIF Formats, and Other Data Formats	p. 271
The Worldwide Protein Data Bank	p. 293
The Nucleic Acid Database	p. 305
Other Structure-Based Databases	p. 321
Data Integrity and Comparative Features	p. 339
Structural Quality Assurance	p. 341
The Impact of Local Accuracy in Protein and RNA Structures: Validation as an Active Tool	p. 377
Structure Comparison and Alignment	p. 397
Protein Structure Evolution and the Scop Database	p. 419
The Cath Domain Structure Database	p. 433
Structural and Functional Assignment	p. 457
Secondary Structure Assignment	p. 459
Identifying Structural Domains in Proteins	p. 485
Inferring Protein Function from Structure	p. 515
Structural Annotation of Genomes	p. 539
Evolution Studied Using Protein Structure	p. 559
Macromolecular Interactions	p. 573
Electrostatic Interactions	p. 575
Prediction of Protein-Nucleic Acid Interactions	p. 593
Prediction of Protein-Protein Interactions from Evolutionary Information	p. 615
Docking Methods, Ligand Design, and Validating Data Sets in the Structural Genomics Era	p. 633
Structure Prediction	p. 663
Casp and Other Community-Wide Assessments to Advance the Field of Structure Prediction	p. 665
Prediction of Protein Structure in 1D: Secondary Structure, Membrane Regions, and Solvent Accessibility	p. 679
Homology Modeling	p. 715
Fold Recognition Methods	p. 733
De Novo Protein Structure Prediction: Methods and Application	p. 755
RNA Structural Bioinformatics	p. 791
Therapeutic Discovery	p. 807
Structural Bioinformatics in Drug Discovery	p. 809
B-Cell Epitope Prediction	p. 847
Future Challenges	p. 879
Methods to Classify and Predict the Structure of Membrane Proteins	p. 881
Protein Motion: Simulation	p. 907
The Significance and Impacts of Protein Disorder and Conformational Variants	p. 937
Protein Designability and Engineering	p. 961
Structural Genomics of Protein Superfamilies	p. 983
Index	p. 1019
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