Protein Simulations: Advances in Protein Chemistry
Regular price
64.750 KD
inc. VAT
Couldn't load pickup availability
Table of contents
- Contentsv
- Prefaceix
- Chapter 1. Assessment of the Role of Computations in Structural Biology1
- I. Introduction1
- II. Comparison of the Role of Computation in the Study of Small Molecules and Macromolecules2
- III. Comparison of Theory and Experiment5
- IV. Molecular Recognition and Docking8
- V. Error Estimation and Error Propagation in Experiment and Theory10
- VI. The Role of Models in Protein Simulations13
- VII. Parameterization15
- VIII. Testing of Theoretical Models for Structural Biology16
- IX. Conclusions19
- References19
- Chapter 2. Force Fields for Protein Simulations27
- I. Introduction27
- II. Protein Force Fields, 1980 to the Present30
- III. Beyond Fixed Atomic Point-Charge Electrostatics45
- IV. Modeling the Solvent Environment62
- V. Conclusions77
- References78
- Chapter 3. Protein Simulation and Drug Design87
- I. Introduction87
- II. Fixed-Conformation Models88
- III. Including Protein and Ligand Flexibility in Modeling Molecular Recognition95
- IV. Fast Approximate Simulation Methods for Calculating Binding Free Energies103
- V. Including Protein Flexibility in Virtual Screening111
- VI. Enhanced Sampling via the Replica-Exchange Method115
- VII. Conclusions117
- References118
- Chapter 4. Free Energy Calculations and Ligand Binding123
- I. Introduction123
- II. Free Energy Perturbation and Thermodynamic Integration125
- III. Extrapolation of Free Energies135
- IV. Linear Interaction Energy Approaches137
- V. MM-PBSA147
- VI. PROFEC149
- VII. Dynamics and Chemical MC/MD151
- VIII. Conclusions154
- References155
- Chapter 5. Membrane Protein Simulations: Ion Channels and Bacterial Outer Membrane Proteins159
- I. Introduction159
- II. Simulation Methods162
- III. Ion Channels166
- IV. Outer Membrane Proteins174
- V. Future Prospects183
- References185
- Chapter 6. Large Scale Simulation of Protein Mechanics and Function195
- I. Introduction195
- II. Technology for Simulation and Visualization of Large Biomolecular Systems198
- III. Aquaporins–Membrane Water Channels201
- IV. Energy Conversion in ATP Synthase211
- V. Mechanical Signaling in Fibronectin232
- VI. Outlook237
- References239
- Chapter 7. Structure/Function Correlations of Proteins Using MM, QM/MM and Related Approaches: Metho249
- I. Introduction249
- II. Classical Force Fields and Their Use250
- III. Evaluation of Electrostatic Free Energies of Macromolecules258
- IV. Methods for Simulation of Chemical Processes in Enzymes263
- V. Studying Enzyme Catalysis274
- VI. Concluding Remarks301
- References302
- Chapter 8. Catalysis and Specificity in Enzymes: A Study of Triosephosphate Isomerase and Comparison315
- I. Introduction315
- II. Computational Methods320
- III. Preparation of the Active Site: The TIM ‘‘Lid’’ Transition324
- IV. Analysis of Mechanisms of the TIM Catalyzed Reactions: The Effect on the Activation Barrier327
- V. Dynamic Effects in the TIM Reaction344
- VI. Catalytic Specificity: Comparison of TIM and MGS358
- VII. Conclusions366
- References368
- Chapter 9. All-Atom Simulations of Protein Folding and Unfolding373
- I. Background373
- II. Overview of Results377
- III. Conclusions/Summary395
- References399
- Author Index405
- Subject Index429
- Color Plate SectionPlate-1
Protein Simulation focuses on predicting how protein will act in vivo. These studies use computer analysis, computer modeling, and statistical probability to predict protein function.
* Force Fields
* Ligand Binding
* Protein Membrane Simulation
* Enzyme Dynamics
* Protein Folding and unfolding simulations
* Force Fields
* Ligand Binding
* Protein Membrane Simulation
* Enzyme Dynamics
* Protein Folding and unfolding simulations