Structural Bioinformatics (eBook, ePUB)

Redaktion: Gu, Jenny; Bourne, Philip E.

• Format: ePub

Produktbeschreibung

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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Produktdetails

• Verlag: John Wiley & Sons
• Seitenzahl: 1072
• Erscheinungstermin: 20. September 2011
• Englisch
• ISBN-13: 9781118210567
• Artikelnr.: 37340933

Autorenporträt

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.

Inhaltsangabe

Foreword. Preface. Acknowledgments. Contributors. Section I DATA COLLECTION
ANALYSIS
AND VISUALIZATION. 1 DEFINING BIOINFORMATICS AND STRUCTURAL BIOINFORMATICS (Russ B. Altman and Jonathan M. Dugan). 2 FUNDAMENTALS OF PROTEIN STRUCTURE (Eric D. Scheeff and J. Lynn Fink). 3 FUNDAMENTALS OF DNA AND RNA STRUCTURE (Stephen Neidle
Bohdan Schneider
and Helen M. Berman). 4 COMPUTATIONAL ASPECTS OF HIGH-THROUGHPUT CRYSTALLOGRAPHIC MACROMOLECULAR STRUCTURE DETERMINATION (Paul D. Adams
Ralf W. Grosse-Kunstleve
and Axel T. Brunger). 5 MACROMOLECULAR STRUCTURE DETERMINATION BY NMR SPECTROSCOPY (John L. Markley
Arash Bahrami
Hamid R. Eghbalnia
Francis C. Peterson
Robert C. Tyler
Eldon L. Ulrich
William M. Westler
and Brian F. Volkman). 6 ELECTRON MICROSCOPY IN THE CONTEXT OF STRUCTURAL SYSTEMS BIOLOGY (Niels Volkmann and Dorit Hanein). 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 (Sheng Li
Dmitri Mouradov
Gordon King
Tong Liu
Ian Ross
Bostjan Kobe
Virgil L. Woods Jr
and Thomas Huber). 8 SEARCH AND SAMPLING IN STRUCTURAL BIOINFORMATICS (Ilan Samish). 9 MOLECULAR VISUALIZATION (Steven Bottomley and Erik Helmerhorst). Section II DATA REPRESENTATION AND DATABASES. 10 THE PDB FORMAT
mmCIF FORMATS
AND OTHER DATA FORMATS (John D. Westbrook and Paula M.D. Fitzgerald). 11 THE WORLDWIDE PROTEIN DATA BANK (Helen M. Berman
Kim Henrick
Haruki Nakamura
and John L. Markley). 12 THE NUCLEIC ACID DATABASE (Bohdan Schneider
Joanna de la Cruz
Zukang Feng
Li Chen
Shuchismita Dutta
Irina Persikova
John D. Westbrook
Huanwang Yang
Jasmine Young
Christine Zardecki
and Helen M. Berman). 13 OTHER STRUCTURE-BASED DATABASES (J. Lynn Fink
Helge Weissig
and Philip E. Bourne). Section III DATA INTEGRITY AND COMPARATIVE FEATURES. 14 STRUCTURAL QUALITY ASSURANCE (Roman A. Laskowski). 15 THE IMPACT OF LOCAL ACCURACY IN PROTEIN AND RNA STRUCTURES: VALIDATION AS AN ACTIVE TOOL (Jane S. Richardson and David C. Richardson). 16 STRUCTURE COMPARISON AND ALIGNMENT (Marc A. Marti-Renom
Emidio Capriotti
Ilya N. Shindyalov
and Philip E. Bourne). 17 PROTEIN STRUCTURE EVOLUTION AND THE SCOP DATABASE (Raghu P. R. Metpally and Boojala V. B. Reddy). 18 THE CATH DOMAIN STRUCTURE DATABASE (Frances M. G. Pearl
Alison Cuff
and Christine A. Orengo). Section IV STRUCTURAL AND FUNCTIONAL ASSIGNMENT. 19 SECONDARY STRUCTURE ASSIGNMENT (Claus A. Andersen and Burkhard Rost). 20 IDENTIFYING STRUCTURAL DOMAINS IN PROTEINS (Stella Veretnik
Jenny Gu
and Shoshana Wodak). 21 INFERRING PROTEIN FUNCTION FROM STRUCTURE (James D. Watson
Gail J. Bartlett
and Janet M. Thornton). 22 STRUCTURAL ANNOTATION OF GENOMES (Adam J. Reid
Corin Yeats
Jonathan Lees
and Christine A. Orengo). 23 EVOLUTION STUDIED USING PROTEIN STRUCTURE (Song Yang
Ruben Valas
and Philip E. Bourne). Section V MACROMOLECULAR INTERACTIONS. 24 ELECTROSTATIC INTERACTIONS (Nathan A. Baker and J. Andrew McCammon). 25 PREDICTION OF PROTEIN-NUCLEIC ACID INTERACTIONS (Timothy Robertson and Gabriele Varani). 26 PREDICTION OF PROTEIN-PROTEIN INTERACTIONS FROM EVOLUTIONARY INFORMATION (Alfonso Valencia and Florencio Pazos). 27 DOCKING METHODS
LIGAND DESIGN
AND VALIDATING DATA SETS IN THE STRUCTURAL GENOMICS ERA (Natasja Brooijmans). Section VI STRUCTURE PREDICTION. 28 CASP AND OTHER COMMUNITY-WIDE ASSESSMENTS TO ADVANCE THE FIELD OF STRUCTURE PREDICTION (Jenny Gu and Philip E. Bourne). 29 PREDICTION OF PROTEIN STRUCTURE IN 1D: SECONDARY STRUCTURE
MEMBRANE REGIONS
AND SOLVENT ACCESSIBILITY (Burkhard Rost). 30 HOMOLOGY MODELING (Hanka Venselaar
Elmar Krieger
and Gert Vriend). 31 FOLD RECOGNITION METHODS (Adam Godzik). 32 DE NOVO PROTEIN STRUCTURE PREDICTION: METHODS AND APPLICATION (Kevin Drew
Dylan Chivian
and Richard Bonneau). 33 RNA STRUCTURAL BIOINFORMATICS (Magdalena A. Jonikas
Alain Laederach
and Russ B. Altman). Section VII THERAPEUTIC DISCOVERY. 34 STRUCTURAL BIOINFORMATICS IN DRUG DISCOVERY (William R. Pitt
Al1¿cia Perez Higueruelo
and Colin R. Groom). 35 B-CELL EPITOPE PREDICTION (Julia V. Ponomarenko and Marc H.V. van Regenmortel). Section VIII FUTURE CHALLENGES. 36 METHODS TO CLASSIFY AND PREDICT THE STRUCTURE OF MEMBRANE PROTEINS (Marialuisa Pellegrini-Calace and Janet M. Thornton). 37 PROTEIN MOTION: SIMULATION (Ilan Samish
Jenny Gu
and Michael L. Klein). 38 THE SIGNIFICANCE AND IMPACTS OF PROTEIN DISORDER AND CONFORMATIONAL VARIANTS (Jenny Gu and Vincent J. Hilser). 39 PROTEIN DESIGNABILITY AND ENGINEERING (Nikolay V. Dokholyan). 40 STRUCTURAL GENOMICS OF PROTEIN SUPERFAMILIES (Stephen K. Burley
Steven C. Almo
Jeffrey B. Bonanno
Mark R. Chance
Spencer Emtage
Andras Fiser
Andrej Sali
J. Michael Sauder
and Subramanyam Swaminathan). INDEX.