Book description
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
Table of contents
- Cover
- Title Page
- Copyright
- Foreword
- Contributors
-
Section I DATA COLLECTION, ANALYSIS, AND VISUALIZATION
- 1 DEFINING BIOINFORMATICS AND STRUCTURAL BIOINFORMATICS
-
2 FUNDAMENTALS OF PROTEIN STRUCTURE
- THE IMPORTANCE OF PROTEIN STRUCTURE
- THE PRIMARY STRUCTURE OF PROTEINS: THE AMINO ACID SEQUENCE
- THE SECONDARY STRUCTURE OF PROTEINS: THE LOCAL THREE-DIMENSIONAL STRUCTURE
- THE TERTIARY STRUCTURE OF PROTEINS: THE GLOBAL THREE-DIMENSIONAL STRUCTURE
- THE QUATERNARY STRUCTURE OF PROTEINS: ASSOCIATIONS OF MULTIPLE POLYPEPTIDE CHAINS
- CONCLUSION
- MORE INFORMATION ON THE INTERNET
- REFERENCES
- 3 FUNDAMENTALS OF DNA AND RNA STRUCTURE
- 4 COMPUTATIONAL ASPECTS OF HIGH-THROUGHPUT CRYSTALLOGRAPHIC MACROMOLECULAR STRUCTURE DETERMINATION
- 5 MACROMOLECULAR STRUCTURE DETERMINATION BY NMR SPECTROSCOPY
- 6 ELECTRON MICROSCOPY IN THE CONTEXT OF STRUCTURAL SYSTEMS BIOLOGY
-
7 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
- INTRODUCTION
- OVERVIEW OF DXMS METHODOLOGY
- EXAMPLES OF APPLICATIONS OF DXMS
- DXMS ANALYSIS: CONCLUDING REMARKS
- HYBRID BIOCHEMICAL/BIOINFORMATICS APPROACH TO LOWRESOLUTION STRUCTURE DETERMINATION USING CHEMICAL CROSS-LINKERS AND MASS SPECTROMETRY
- RECENT APPLICATIONS
- CONCLUSION WITH RESPECT TO CHEMICAL CROSS-LINKAGE METHODS
- ACKNOWLEDGMENTS
- REFERENCES
- 8 SEARCH AND SAMPLING IN STRUCTURAL BIOINFORMATICS
- 9 MOLECULAR VISUALIZATION
- Section II DATA REPRESENTATION AND DATABASES
-
Section III DATA INTEGRITY AND COMPARATIVE FEATURES
-
14 STRUCTURAL QUALITY ASSURANCE
- INTRODUCTION
- STRUCTURES AS MODELS
- AIMS
- ERROR ESTIMATION AND PRECISION
- ERROR ESTIMATES IN X-RAY CRYSTALLOGRAPHY
- ERROR ESTIMATES IN NMR SPECTROSCOPY
- ERRORS IN DEPOSITED STRUCTURES
- STEREOCHEMICAL PARAMETERS
- SOFTWARE FOR QUALITY CHECKS
- PROCHECK
- WHAT_CHECK
- QUALITY INFORMATION ON THE WEB
- PDBREPORT–WHAT_CHECK Results
- CONCLUSIONS
- ACKNOWLEDGMENTS
- REFERENCES
- 15 THE IMPACT OF LOCAL ACCURACY IN PROTEIN AND RNA STRUCTURES: VALIDATION AS AN ACTIVE TOOL
-
16 STRUCTURE COMPARISON AND ALIGNMENT
- INTRODUCTION
- GENERAL APPROACH TO STRUCTURE COMPARISON AND ALIGNMENT
- COMPARISON ALGORITHM AND OPTIMIZATION
- HOW WELL ARE WE DOING?
- SAMPLE RESULTS FROM STRUCTURE COMPARISON AND ALIGNMENT
- MULTIPLE STRUCTURE ALIGNMENT
- FLEXIBLE STRUCTURE ALIGNMENT
- MAPPING PROTEIN FOLD SPACE
- THE IMPACT OF STRUCTURAL GENOMICS
- THE FUTURE
- ACKNOWLEDGMENTS
- REFERENCES
-
17 PROTEIN STRUCTURE EVOLUTION AND THE SCOP DATABASE
- INTRODUCTION
- THE EVOLUTION OF PROTEINS
- THE EVOLUTION OF FOLD
- THE EVOLUTION OF ENZYMATIC CATALYSIS
- THE COMPARISON OF STRUCTURES
- SCOP HIERARCHY
- CLASSES
- FOLDS
- SUPERFAMILIES
- FAMILIES
- ORGANIZATION AND CAPABI LITIES OF THE SCOP RESOURCE
- BROWSING THROUGH THE SCOP HIERARCHY
- LINKING TO OTHER STRUCTURE AND SEQUENCE DATABASES
- SCOP REFINEMENTS TO ACCOMMODATE STRUCTURAL GENOMICS
- NEW FEATURES IN SCOP
- INTEGRATION WITH OTHER DATABASES
- RECLASSIFICATION
- SCOP USAGE
- SCOP FROM A USER’S PERSPECTIVE
- REFERENCES
-
18 THE CATH DOMAIN STRUCTURE DATABASE
- INTRODUCTION
- HISTORICAL DEVELOPMENT
- CURRENT METHODOLOGIES FOR IDENTIFYING STRUCTURAL SIMILARITIES AND EVOLUTIONARY RELATIONSHIPS IN CATH
- CLASSIFYING CLOSE HOMOLOGUES (CHOPCLOSE)
- IDENTIFICATION OF DOMAIN BOUNDARIES
- METHODS TO DETECT SEQUENCE AND STRUCTURAL RELATIVES
- STRUCTURE-BASED METHODS FOR IDENTIFYING STRUCTURAL HOMOLOGUES AND RELATED FOLDS (SSAP AND CATHEDRAL)
- SSAP—SEQUENTIAL STRUCTURE ALIGNMENT PROGRAM
- CATHEDRAL—CATHS EXISTING DOMAIN RECOGNITION ALGORITHM
- METHODS FOR GENERATING MULTIPLE STRUCTURE ALIGNMENTS (CORA) AND PROTOCOLS FOR USING 3D TEMPLATES USED TO IDENTIFY DISTANT STRUCTURAL RELATIONSHIPS
- SEQUENCE, STRUCTURAL, AND FUNCTIONAL VALIDATION OF HOMOLOGY
- THE DICTIONARY OF HOMOLOGOUS SUPERFAMILIES (DHS)
- THE GENE3D RESOURCE
- THE CATH WEB SITE AND SERVER
- THE CATHEDRAL SERVER
- IS FOLD CLASSIFICATION A LEGITIMATE REPRESENTATION OF DOMAIN STRUCTURE SPACE?
- POPULATION OF SUPERFAMILIES AND FAMILIES WITHIN FOLDS
- FOLD CLASSIFICATION IN CATH
- ACKNOWLEDGMENTS
- REFERENCES
-
14 STRUCTURAL QUALITY ASSURANCE
-
Section IV STRUCTURAL AND FUNCTIONAL ASSIGNMENT
- 19 SECONDARY STRUCTURE ASSIGNMENT
-
20 IDENTIFYING STRUCTURAL DOMAINS IN PROTEINS
- INTRODUCTION
- DEFINITIONS OF STRUCTURAL DOMAINS
- ALGORITHMS FOR IDENTIFYING STRUCTURAL DOMAINS: INSIGHT INTO HISTORY AND METHODOLOGY
- ALGORITHMS FOR IDENTIFYING STRUCTURAL DOMAINS: IN-DEPTH
- DOMAIN ASSIGNMENTS: EVALUATING AUTOMATIC METHODS
- DOMAIN PREDICTION BASED ON SEQUENCE INFORMATION
- CONCLUSIONS AND PERSPECTIVES
- WEB RESOURCES
- REFERENCES
- 21 INFERRING PROTEIN FUNCTION FROM STRUCTURE
-
22 STRUCTURAL ANNOTATION OF GENOMES
- INTRODUCTION
- AVAILABILITY OF COMPLETED GENOMES
- METHODOLOGIES FOR IDENTIFYING STRUCTURAL PROTEIN DOMAINS IN GENOMES
- HOW WELL ARE GENOMES COVERED BY STRUCTURAL DOMAIN ANNOTATION?
- CAN WE DETERMINE ALL THE STRUCTURES PRESENT IN THE GENOMES?—STRUCTURAL ANNOTATION OF GENOMES AND STRUCTURAL GENOMICS
- WHAT CAN STRUCTURAL GENOME ANNOTATION TELL US ABOUT EVOLUTION?
- STRUCTURAL GENOME ANNOTATION RESOURCES
- SUPERFAMILY
- 3D GENOMICS
- SUMMARY
- REFERENCES
- 23 EVOLUTION STUDIED USING PROTEIN STRUCTURE
- Section V MACROMOLECULAR INTERACTIONS
-
Section VI STRUCTURE PREDICTION
- 28 CASP AND OTHER COMMUNITY-WIDE ASSESSMENTS TO ADVANCE THE FIELD OF STRUCTURE PREDICTION
- 29 PREDICTION OF PROTEIN STRUCTURE IN 1D: SECONDARY STRUCTURE, MEMBRANE REGIONS, AND SOLVENT ACCESSIBILITY
- 30 HOMOLOGY MODELING
- 31 FOLD RECOGNITION METHODS
- 32 DE NOVO PROTEIN STRUCTURE PREDICTION: METHODS AND APPLICATION
- 33 RNA STRUCTURAL BIOINFORMATICS
-
Section VII THERAPEUTIC DISCOVERY
- 34 STRUCTURAL BIOINFORMATICS IN DRUG DISCOVERY
-
35 B-CELL EPITOPE PREDICTION
- INTRODUCTION
- THE PROBLEM OF B-CELL EPITOPE PREDICTION
- ANTIBODY STRUCTURE AND FUNCTION
- EXPERIMENTAL METHODS USED FOR B-CELL EPITOPE IDENTIFICATION
- HISTORY OF ATTEMPTS AT B-CELL EPITOPE PREDICTION
- BIOINFORMATICS METHODS FOR B-CELL EPITOPE PREDICTION
- APPLICATIONS
- CONCLUSION
- ABBREVIATIONS
- ACKNOWLEDGMENT
- REFERENCES
-
Section VIII FUTURE CHALLENGES
-
36 METHODS TO CLASSIFY AND PREDICT THE STRUCTURE OF MEMBRANE PROTEINS
- THE BIOLOGICAL MEMBRANE
- THE FOLDING PROCESS OF MEMBRANE PROTEINS
- WHY IS IT DIFFICULT TO SOLVE MEMBRANE PROTEIN 3D STRUCTURES?
- STRUCTURAL GENOMICS AND MEMBRANE PROTEINS
- COMPUTATIONAL METHODS FOR THE IDENTIFICATION OF MEMBRANE PROTEINS AND THE PREDICTION OF THEIR STRUCTURES
- WEB-AVAILABLE DATA RESOURCES FOR MEMBRANE PROTEINS
- CLASSIFICATION OF MEMBRANE PROTEINS
- CONCLUSIONS
- REFERENCES
- 37 PROTEIN MOTION: SIMULATION
- 38 THE SIGNIFICANCE AND IMPACTS OF PROTEIN DISORDER AND CONFORMATIONAL VARIANTS
- 39 PROTEIN DESIGNABILITY AND ENGINEERING
-
40 STRUCTURAL GENOMICS OF PROTEIN SUPERFAMILIES
- INTRODUCTION
- NYSGXRC
- BIOMEDICAL THEME TARGETS: BACKGROUND AND MOTIVATION
- BIOMEDICAL THEME TARGETS: SELECTION AND PROGRESS
- BIOMEDICAL THEME TARGETS: SELECTED EXAMPLES
- PROTEIN TYROSINE PHOSPHATASE (PTPs)
- INSULINOMA-ASSOCIATED PROTEIN 2 (IA-2)
- SMALL C-TERMINAL DOMAIN PHOSPHATASE 3
- CHRONOPHIN
- OTHER PHOSPHATASES
- BIOMEDICAL THEME TARGETS: POTENTIAL IMPACT ON DRUG DISCOVERY
- FRAGMENT CONDENSATION LEAD DISCOVERY STRATEGY APPLIED TO PTP1B
- VIRTUAL SCREENING STRATEGY APPLIED TO PP2Cα
- BIOMEDICAL THEME TARGETS: CONCLUSION
- COMMUNITY-NOMINATED TARGETS: MOTIVATION
- COMMUNITY-NOMINATED TARGETS: SELECTION AND PROGRESS
- COMMUNITY-NOMINATED TARGETS: FUNCTIONAL CHARACTERIZATION
- COMMUNITY-NOMINATED TARGETS: CONCLUSION
- OVERALL CONCLUSIONS
- ACKNOWLEDGMENTS
- REFERENCES
-
36 METHODS TO CLASSIFY AND PREDICT THE STRUCTURE OF MEMBRANE PROTEINS
- INDEX
Product information
- Title: Structural Bioinformatics, 2nd Edition
- Author(s):
- Release date: March 2009
- Publisher(s): Wiley-Blackwell
- ISBN: 9781118210567
You might also like
book
Bioinformatics and Functional Genomics, Second Edition
The bestselling introduction to bioinformatics and functional genomics—now in an updated edition Widely received in its …
book
Bioinformatics
Life science data integration and interoperability is one of the most challenging problems facing bioinformatics today. …
book
Bioinformatics and Medical Applications
BIOINFORMATICS AND MEDICAL APPLICATIONS The main topics addressed in this book are big data analytics problems …
book
Bioinformatics for Biomedical Science and Clinical Applications
Contemporary biomedical and clinical research is undergoing constant development thanks to the rapid advancement of various …