Structural bioinformatics / edited by Philip E. Bourne, Helge Weissig.

Format:

Book

Contributor:

Bourne, Philip E.

Weissig, Helge.

Series:

Methods of biochemical analysis ; v. 44.

Methods of biochemical analysis ; v. 44

Language:

English

Subjects (All):

Macromolecules--Structure--Mathematical models.

Macromolecules.

Macromolecules--Structure--Computer simulation.

Bioinformatics.

Computational Biology.

Macromolecules--Structure.

Computer simulation.

Mathematical models.

Medical Subjects:

Computational Biology.

Physical Description:

xix, 649 pages, 32 unnumbered pages of plates : illustrations (some color) ; 26 cm.

Place of Publication:

Hoboken, N.J. : Wiley-Liss, [2003]

Summary:

"This collection ... is a must-read for all of us committed to understanding the interplay of structure and function ... [T]he individual chapters outline the suite of major basic life science questions such as the status of efforts to predict protein structure and how proteins carry out cellular functions, and also the applied life science questions such as how structural bioinformatics can improve health care through accelerating drug discovery." - From the Foreword by John C. Wooley

As genomic and post-genomic innovations revolutionize the biological sciences, three-dimensional structural data continues to prove of vital importance to understanding function. Structural Bioinformatics represents an unprecedented, comprehensive account of the state of the discipline, providing an essential resource for students and practitioners.

Philip Bourne and Helge Weissig's authoritative text delivers a basic understanding of the theories, associated algorithms, resources, and tools used in structural bioinformatics. Among other topics, the book covers: Fundamentals of protein structure X-ray crystallography Molecular visualization Structure classification of proteins (SCOP) Class, architecture, topology, and homology (CATH) classification Proteins as drug targets

Practicing researchers as well as students in biology, medicine, and computer science will find Structural Bioinformatics to be this field's premier resource.

Contents:

1 Defining Bioinformatics and Structural Bioinformatics / Russ B. Altman, Jonathan M. Dugan 3

2 Fundamentals of Protein Structure / Eric D. Scheeff, J. Lynn Fink 15

3 Fundamentals of DNA and RNA Structure / Stephen Neidle, Bohdan Schneider, Helen M. Berman 41

4 Computational Aspects of High-Throughput Crystallographic Macromolecular Structure Determination / Paul D. Adams, Ralf W. Grosse-Kunstleve, Axel T. Brunger 75

5 Macromolecular Structure Determination By NMR Spectroscopy / John L. Markley, Eldon L. Ulrich, William M. Westler, Brian F. Volkman 89

6 Electron Microscopy / Niels Volkmann, Dorit Hanein 115

7 Molecular Visualization / John Tate 135

Section II Data Representation and Databases 159

8 The PDB Format, mmCIF Formats, and other Data Formats / John D. Westbrook, P. M. D. Fitzgerald 161

9 The Protein Data Bank / The PDB Team 181

10 The Nucleic Acid Database / Helen M. Berman, John Westbrook, Zukang Feng, Lisa Iype, Bohdan Schneider, Christine Zardecki 199

11 Other Structure-Based Databases / Helge Weissig, Philip E. Bourne 217

Section III Comparative Features 237

12 Protein Structure Evolution and the Scop Database / Boojala V. B. Reddy, Philip E. Bourne 239

13 The Cath Domain Structure Database / C. A. Orengo, F. M. G. Pearl, J. M. Thornton 249

14 Structural Quality Assurance / Roman A. Laskowski 273

15 All-Atom Contacts: A New Approach to Structure Validation / Jane S. Richardson 305

16 Structure Comparison and Alignment / Philip E. Bourne, Ilya N. Shindyalov 321

Section IV Structure and Functional Assignment 339

17 Secondary Structure Assignment / Claus A. F. Andersen, Burkhard Rost 341

18 Identifying Structural Domains in Proteins / Lorenz Wernisch, Shoshana J. Wodak 365

19 Inferring Protein Function from Structure / Gail J. Bartlett, Annabel E. Todd, Janet M. Thornton 387

Section V Protein Interactions 409

20 Prediction of Protein-Protein Interactions from Evolutionary Information / Alfonso Valencia, Florencio Pazos 411

21 Electrostatic Interactions / Nathan A. Baker, J. Andrew McCammon 427

Section VI Proteins as Drug Targets 441

22 Principles and Methods of Docking and Ligand Design / J. Krumrine, F. Raubacher, N. Brooijmans, I. Kuntz 443

23 Structural Bioinformatics in Drug Discovery / Eric B. Fauman, Andrew L. Hopkins, Colin R. Groom 477

Section VII Structure Prediction 499

24 Casp and Cafasp Experiments and Their Findings / Philip E. Bourne 501

25 Homology Modeling / Elmar Krieger, Sander B. Nabuurs, Gert Vriend 509

26 Fold Recognition Methods / Adam Godzik 525

27 AB Initio Methods / Dylan Chivian, Timothy Robertson, Richard Bonneau, David Baker 547

28 Prediction in 1D: Secondary Structure, Membrane Helices, and Accessibility / Burkhard Rost 559

Section VIII The Future 589

29 Structural Genomics / Stephen K. Burley, Jeffrey B. Bonanno 591.

Notes:

Includes bibliographical references and index.

ISBN:

0471202002

0471201995

OCLC:

50199108