Computational Biochemistry and Biophysics

Oren M. Becker, Alexander D. MacKerell, Benoît Roux, Masakatsu Watanabe

"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

• Computational methods: atomistic models and force fields; dynamics methods; conformational analysis; treatment of long-range forces and potential; internal co-ordinate simulation method; implicit solvent models; normal mode analysis of biological molecules; free energy calculations; reaction rates and transition pathways; computer simulation of biochemical reactions with QM-MM methods. Experimental data analysis: X-ray and neutron scattering as probes of the dynamics of biological molecules; applications of molecular modelling in NMR structure determination. Modelling and design: comparative protein structure modelling; Bayesian statistics in molecular and structural biology. Computer-aided drug design. Advanced applications: protein folding; simulations of electron transfer proteins; the RISM-SCF/MCSCF approach for the chemical processes in solutions; nucleic acids simulations; membrane simulations. Appendix: useful Web sites.