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Contributors pagevii
Preface ix

1 Progress and issues for computationally guided lead discovery and optimization 1
William L. Jorgensen

PART I. STRUCTURAL BIOLOGY

2 X-ray crystallography in the service of structure-based drug design 17
Gregory A. Petsko and Dagmar Ringe

3 Fragment-based structure-guided drug discovery: strategy, process, and lessons
from human protein kinases 30
Stephen K. Burley, Gavin Hirst, Paul Sprengeler, and Siegfried Reich

4 NMR in fragment-based drug discovery 41
Christopher A. Lepre, Peter J. Connolly, and Jonathan M. Moore
PART II. COMPUTATIONAL CHEMISTRY METHODOLOGY

5 Free-energy calculations in structure-based drug design 61
Michael R. Shirts, David L. Mobley, and Scott P. Brown

6 Studies of drug resistance and the dynamic behavior of HIV-1 protease through
molecular dynamics simulations 87
Fangyu Ding and Carlos Simmerling

7 Docking: a domesday report 98
Martha S. Head

8 The role of quantum mechanics in structure-based drug design 120
Kenneth M. Merz, Jr.

9 Pharmacophore methods 137
Steven L. Dixon

10 QSAR in drug discovery 151
Alexander Tropsha

11 Predicting ADME properties in drug discovery 165
William J. Egan

PART III: APPLICATIONS TO DRUG DISCOVERY

12 Computer-aided drug design: a practical guide to protein-structure-based modeling 181
Charles H. Reynolds

13 Structure-based drug design case study: p38 197
Arthur M. Doweyko

14 Structure-based design of novel P2-P4 macrocyclic inhibitors of hepatitis
C NS3/4A protease 209
M. Katharine Holloway and Nigel J. Liverton

15 Purine nucleoside phosphorylases as targets for transition-state analog design 215
Andrew S. Murkin and Vern L. Schramm

16 GPCR 3D modeling 248
Frank U. Axe

17 Structure-based design of potent glycogen phosphorylase inhibitors 257
Qiaolin Deng，

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