Becker O.M., MacKerell A.D. et al. Computational Biochemistry and Biophysics

CRC Press, 2001. — 512 p. — ISBN 0824741404, 9780824741402.The book provides the needed information for calculating and interpreting experimentally observed properties on the basis of the results generated by computer simulations. This book is organized so that nonspecialists as well as more advanced users can benefit. It can serve as both an introductory text to computational biology, making it useful for students, and a reference source for active researchers in the field. We have tried to compile a comprehensive but reasonably concise review of relevant theoretical and computational methods that is self-contained. Therefore, the chapters, particularly in Part I, are ordered so that the reader can easily follow from one topic to the next and be systematically introduced to the theoretical methods used in computational studies of biomolecular systems. The remainder of the book is designed so that the individual parts as well as their chapters can be read independently. Additional technical details can be found in the references listed in each chapter. Thus the book may also serve as a useful reference for both theoreticians and experimentalists in all areas of biophysics and biochemical research.
This volume thus presents a current and comprehensive account of computational methods and their application to biological macromolecules. We hope that it will serve as a useful tool to guide future investigations of proteins, nucleic acids, and biological membranes, so that the mysteries of biological molecules can continue to be revealed.Computational MethodsAtomistic Models and Force Fields
Dynamics Methods
Conformational Analysis
Treatment of Long-Range Forces and Potential
Internal Coordinate 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 Modeling in NMR Structure Determination
Modeling and Design
Comparative Protein Structure Modeling
Bayesian Statistics in Molecular and Structural Biology
Computer Aided Drug Design
Advanced Applications
Protein Folding: Computational Approaches
Simulations of Electron Transfer Proteins
The RISM-SCF/MCSCF Approach for Chemical Processes in Solutions
Nucleic Acid Simulations
Membrane Simulations