Computational Biochemistry and Biophysics

Front Cover
Oren M. Becker, Alexander D. MacKerell Jr., Benoit Roux, Masakatsu Watanabe
CRC Press, Feb 9, 2001 - Science - 512 pages
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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.
 

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Contents

1 Introduction
1
2 Atomistic Models and Force Fields
7
3 Dynamics Methods
39
4 Conformational Analysis
69
5 Treatment of LongRange Forces and Potential
91
6 Internal Coordinate Simulation Method
115
7 Implicit Solvent Models
133
8 Normal Mode Analysis of Biological Molecules
153
13 Applications of Molecular Modeling in NMR Structure Determination
253
14 Comparative Protein Structure Modeling
275
15 Bayesian Statistics in Molecular and Structural Biology
313
16 Computer Aided Drug Design
351
Computational Approaches
371
18 Simulations of Electron Transfer Proteins
393
19 The RISMSCFMCSCF Approach for Chemical Processes in Solutions
417
20 Nucleic Acid Simulations
441

9 Free Energy Calculations
169
10 Reaction Rates and Transition Pathways
199
11 Computer Simulation of Biochemical Reactions with QMMM Methods
221
12 XRay and Neutron Scattering as Probes of the Dynamics of Biological Molecules
237
21 Membrane Simulations
465
Useful Internet Resources
497
Index
503
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