《Protein Structure Determination, Analysis, and Applications for Drug
Discovery 》D. Chasman (Marcel Dekker, 2003) WW
Contents
Preface v
Contributors xi
Part I Introduction
1. Structural Biology and Structural Genomics: A Federal
Agency Perspective 1
John C. Norvell and Marvin Cassman
Part II Determination
2. Producing Proteins 9
Aled M. Edwards, Cheryl H. Arrowsmith, Raymond Hui,
Fabien Marino, Alexei Savchenko, Ken Yamazaki, and
Adelinda Yee
3. Crystallization of Membrane Proteins 27
R. Michael Garavito
4. Prospects for High-Throughput Structure Determination by
X-Ray Crystallography 55
Frank von Delft, Charles D. Kang, and Duncan E. McRee
5. Prospects for High-Throughput Structure Determination of
Proteins by NMR Spectroscopy 95
Ann E. Ferentz
6. Automated Molecular Replacement 141
Jorge Navaza and Pedro M. Alzari
7. Comparative Protein Structure Modeling 167
Andra′ s Fiser and Andrej Sali
8. Rising Accuracy of Protein Secondary Structure Prediction 207
Burkhard Rost
9. Novel Fold and Ab Initio Methods for Protein Structure
Generation 251
David J. Osguthorpe
Part III Analysis
10. Identifying Errors in Three-Dimensional Protein Models 277
Brian D. Marsden and Ruben A. Abagyan
11. Comparative Analysis and Evolutionary Classification of
Protein Structures 315
Liisa Holm
12. Automated Genome Functional Annotation for Structural
Genomics 349
Sophia Tsoka and Christos A. Ouzounis
13. The Importance of Structure-Based Function Annotation to
Drug Discovery 369
Susan M. Baxter, Stacy Knutson, and Jacquelyn S. Fetrow
14. The Protein Data Bank 389
Helen M. Berman, Philip E. Bourne, John Westbrook,
and Christine Zardecki
15. The European Bioinformatics Institute Macromolecular
Structure Database (E-MSD) 407
Dimitris Dimitropoulos, Peter A. Keller, Kim Henrick,
John Ionides, Eugene Krissinel, Philip McNeil, and
Sameer S. Velankar
Part IV Applications for Drug Discovery
16. Molecular Docking in Structure-Based Design 417
Trevor W. Heritage
17. Use of Pharmacophores in Structure-Based Drug Design 453
Omoshile Clement and Adrea T. Mehl
18. The Structure of Human Interferon-b-1a (Avonex1) and its
Relation to Activity: A Case Study of the Use of Structural
Data in the Arena of Protein Pharmaceuticals 483
Adrian Whitty and Michael Karpusas
19. G-Protein-Coupled Receptors: Diverse Functions and Shared
Mechanisms of Action Interpreted Through the Structure of
Rhodopsin 521
S. Roy Kimura and Daniel I. Chasman
20. Functional Assessment of Amino Acid Variation Caused by
Single-Nucleotide Polymorphisms: A Structural View 561
Daniel I. Chasman
