Computational biochemistry and biophysics
- نوع فایل : کتاب
- زبان : انگلیسی
- مؤلف : Oren M Becker; et al
- ناشر : New York : M. Dekker
- چاپ و سال / کشور: 2001
- شابک / ISBN : 9780824704551
Description
Foreword Martin Karplus iii Preface vii Contributors xi Part I Computational Methods 1. Introduction 1 Oren M. Becker, Alexander D. MacKerell, Jr., Benoıˆt Roux, and Masakatsu Watanabe 2. Atomistic Models and Force Fields 7 Alexander D. MacKerell, Jr. 3. Dynamics Methods 39 Oren M. Becker and Masakatsu Watanabe 4. Conformational Analysis 69 Oren M. Becker 5. Treatment of Long-Range Forces and Potential 91 Thomas A. Darden 6. Internal Coordinate Simulation Method 115 Alexey K. Mazur 7. Implicit Solvent Models 133 Benoıˆt Roux 8. Normal Mode Analysis of Biological Molecules 153 Steven Hayward 9. Free Energy Calculations 169 Thomas Simonson ix x Contents 10. Reaction Rates and Transition Pathways 199 John E. Straub 11. Computer Simulation of Biochemical Reactions with QM–MM Methods 221 Paul D. Lyne and Owen A. Walsh Part II Experimental Data Analysis 12. X-Ray and Neutron Scattering as Probes of the Dynamics of Biological Molecules 237 Jeremy C. Smith 13. Applications of Molecular Modeling in NMR Structure Determination 253 Michael Nilges Part III Modeling and Design 14. Comparative Protein Structure Modeling 275 Andra´s Fiser, Roberto Sa´nchez, Francisco Melo, and Andrej S ˇ ali 15. Bayesian Statistics in Molecular and Structural Biology 313 Roland L. Dunbrack, Jr. 16. Computer Aided Drug Design 351 Alexander Tropsha and Weifan Zheng Part IV Advanced Applications 17. Protein Folding: Computational Approaches 371 Oren M. Becker 18. Simulations of Electron Transfer Proteins 393 Toshiko Ichiye 19. The RISM-SCF/MCSCF Approach for Chemical Processes in Solutions 417 Fumio Hirata, Hirofumi Sato, Seiichiro Ten-no, and Shigeki Kato 20. Nucleic Acid Simulations 441 Alexander D. MacKerell, Jr. and Lennart Nilsson 21. Membrane Simulations 465 Douglas J. Tobias Appendix: Useful Internet Resources 497 Index 503
