Structural Bioinformatics

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

Auteur

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.

Résumé
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

Contenu
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 PREDICTIO…