Computational Biochemistry and Biophysics

Covering theoretical methods and computational techniques in biomolecular research, this book focuses on approaches for the treatment of macromolecules, including proteins, nucleic acids, and bilayer membranes. It uses concepts in free energy calculations, conformational analysis, reaction rates, and transition pathways to calculate and interpret biomolecular properties gleaned from computer-generated membrane simulations. It also demonstrates comparative protein structure modeling, outlines computer-aided drug design, discusses Bayesian statistics in molecular and structural biology, and examines the RISM-SCF/MCSCF approach to chemical processes in solution.

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.

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