Computational Biochemistry and BiophysicsOren M. Becker, Alexander D. MacKerell Jr., Benoit Roux, Masakatsu Watanabe 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. |
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 |
12 XRay and Neutron Scattering as Probes of the Dynamics of Biological Molecules | 237 |
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 |
9 Free Energy Calculations | 169 |
10 Reaction Rates and Transition Pathways | 199 |
11 Computer Simulation of Biochemical Reactions with QMMM Methods | 221 |
20 Nucleic Acid Simulations | 441 |
21 Membrane Simulations | 465 |
Useful Internet Resources | 497 |
Other editions - View all
Computational Biochemistry and Biophysics Oren M Becker,Alexander D Mackerell Jr,Masakatsu Watanabe,Benoit Roux No preview available - 2019 |
Common terms and phrases
acid addition algorithm alignment allow analysis angle applications approach approximation atoms average binding biological bond calculations Chapter charge Chem Chem Phys chemical comparative complex compounds computational conformational constant contributions coordinates corresponding defined density depends derived described detailed determined developed discussed distance distribution effect electron electrostatic equation example experimental Figure first folding force field free energy function geometry given groups hydrogen important integration interactions Karplus limited mechanics methods minimization Mol Biol molecular dynamics molecules motion Nature normal mode obtained optimization parameters partial performed phase Phys Phys Chem position possible potential prediction probability problem properties protein quantum mechanical reaction redox region represent residues sampling scale sequence side similar simulation solution solvation solvent space statistical step structure studies surface techniques temperature theory tion transition values