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