Structural Bioinformatics

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Jenny Gu, Philip E. Bourne
John Wiley & Sons, Mar 16, 2009 - Computers - 1035 pages
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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

 

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Contents

DEFINING BIOINFORMATICS AND STRUCTURAL
3
FUNDAMENTALS OF PROTEIN STRUCTURE
15
FUNDAMENTALS OF DNA AND RNA STRUCTURE
41
COMPUTATIONAL ASPECTS OF HIGHTHROUGHPUT
77
MACROMOLECULAR STRUCTURE DETERMINATION
93
ELECTRON MICROSCOPY IN THE CONTEXT
143
STUDY OF PROTEIN THREEDIMENSIONAL STRUCTURE
171
SEARCH AND SAMPLING IN STRUCTURAL
207
STRUCTURAL ANNOTATION OF GENOMES
539
EVOLUTION STUDIED USING PROTEIN STRUCTURE
559
ELECTROSTATIC INTERACTIONS
575
PREDICTION OF PROTEINNUCLEIC ACID
593
PREDICTION OF PROTEINPROTEIN INTERACTIONS
615
DOCKING METHODS LIGAND DESIGN
633
CASP AND OTHER COMMUNITYWIDE
665
PREDICTION OF PROTEIN STRUCTURE IN
679

MOLECULAR VISUALIZATION
237
THE PDB FORMAT mmCIF FORMATS AND OTHER
271
THE WORLDWIDE PROTEIN DATA BANK
293
THE NUCLEIC ACID DATABASE
305
OTHER STRUCTUREBASED DATABASES
321
STRUCTURAL QUALITY ASSURANCE
341
THE IMPACT OF LOCAL ACCURACY IN PROTEIN
377
STRUCTURE COMPARISON AND ALIGNMENT
397
PROTEIN STRUCTURE EVOLUTION
419
THE CATH DOMAIN STRUCTURE DATABASE
433
SECONDARY STRUCTURE ASSIGNMENT
459
IDENTIFYING STRUCTURAL DOMAINS IN PROTEINS
485
INFERRING PROTEIN FUNCTION FROM STRUCTURE
515
HOMOLOGY MODELING
715
FOLD RECOGNITION METHODS
733
RNA STRUCTURAL BIOINFORMATICS
791
STRUCTURAL BIOINFORMATICS IN DRUG DISCOVERY
809
BCELL EPITOPE PREDICTION
847
METHODS TO CLASSIFY AND PREDICT
881
SIMULATION
907
THE SIGNIFICANCE AND IMPACTS OF PROTEIN
937
PROTEIN DESIGNABILITY AND ENGINEERING
961
STRUCTURAL GENOMICS OF PROTEIN SUPERFAMILIES
983
INDEX
1019
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