Computational Biochemistry and Biophysics

Oren M. Becker is an Assistant Professor at Tel Aviv University, Israel. The author or coauthor of numerous publications, he is the recipient of the Rothschild Postdoctoral Fellowship (1991), the Fulbright Postdoctoral Fellowship (1991), and the Yig'al Alon Fellowship for Outstanding Young Scientists (1994), and a member of the Israel Chemical Society. Professor Becker received the B.A. degree (1987) in philosophy, the B.Sc. degree (1987) in chemistry and physics, and the Ph.D. degree (1991) in theoretical chemistry from the Hebrew University of Jerusalem, Israel. Alexander D. MacKerell, JR. is an Associate Professor at the School of Pharmacy, University of Maryland, Baltimore. The author or coauthor of numerous publications, he is a member of the Federation of American Societies for Experimental Biology, the American Chemical Society, and the International Society of Quantum Biology and Pharmacology, among others. Professor MacKerell received the A.S. degree (1979) in biology from Gloucester County College, Sewell, New Jersey, the B.S. degree (1981) in chemistry from the University of Hawaii, Honolulu, and the Ph.D. degree (1985) from Rutgers University, New Brunswick, New Jersey. Additionally, he was a Postdoctoral Fellow at the Karolinska  Institut, Stockholm, Sweden, and at Harvard University, Cambridge, Massachusetts. Benoit Roux is Professor of Biochemistry and Structural Biology at the Weill Medical College of Cornell University, New York, New York. The author or coauthor of over 70 book chapters and publications, he is the recipient of the Noranda Lecture Award of the Canadian Society for Chemistry (1998) and the Rutherford Medical (1998) from the Royal Society of Canada. Professor Roux received the B.Sc. degree (1981) in physics and the M.Sc. degree (1984) in biophysics from the University of Montreal, Canada, and the Ph.D. degree (1990) in biophysics from Harvard University, Cambridge, Massachusetts. Masakatsu Watanbe is a Scientific Developer at Wavefunction, Inc., Irvine, California. The author of numerous publications, he is a member of the American Physical Society, the American Chemical Society, and the IEEE Computer Society. The recipient of the Harvard Postdoctoral Fellowship (1991) and the Soka Gakkai International Academic and Cultural Contribution Award (1993), Dr. Watanabe received the B.A. degree (1986) in chemistry from West Virginia University, Morgantown, and the Ph.D. degree  (1991) in chemistry from the University of Pennsylvania, Philadelphia.

"From the foreword... ...This volume has an important role to play in the transition of the field from one limited to specialists to the mainstream of molecular biology. The emphasis on an in-depth description of the computational methodology will make the volume useful as an introduction to the field for many people who are doing simulations for the first time....A number of well-chosen 'special topics' involving applications of simulation methods are described....several chapters broaden the perspective of the book by introducing approaches other than molecular dynamics for modeling proteins and their interactions....equally important...is the biophysical aspect of computational biology. I am very pleased to have been given the opportunity to contribute a Foreword to this very useful book. It is a particular pleasure for me to do so because all the editors and fifteen of the authors are alumnae of my research group at Harvard, where molecular dynamics simulations of biomolecules originated. "---Martin Karplus, Laboratoire de chimie Biophysique, ISIS Université Louis Pasteur, Strasbourg, France, and Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MassachusettsPromo Copy

• Foreword, Preface, Contributors, Part I - Computational Methods, 1. Introduction, 2. Atomistic Models and Force Fields, 3. Dynamics Methods, 4. Conformational Analysis, 5. Treatment of Long-Range Forces and Potential, 6. Internal Coordinate Simulation Method, 7. Implicit Solvent Models, 8. Normal Mode Analysis of Biological Molecules, 9. Free Energy Calculations, 10. Reaction Rates and Transition Pathways, 11. Computer Simulation of Biochemical Reactions with QM-MM Methods, Part II - Experimental Data Analysis, 12. X-Ray and Neutron Scattering as Probes of the Dynamics of Biological Molecules, 13. Applications of Molecular Modeling in NMR Structure Determination, Part III - Modeling and Design, 14. Comparative Protein Structure Modeling, 15. Bayesian Statistics in Molecular and Structural Biology, 16. Computer Aided Drug Design, Part IV - Advanced Applications, 17. Protein Folding: Computational Approaches, 18. Simulations of Electron Transfer Proteins, 19. The RISM-SCF/MCSCF Approach for Chemical Processes in Solutions, 20. Nucleic Acid Simulations, 21. Membrane Simulations, Appendix: Useful Internet Resources, Index