Ulteriori informazioni
The Reviews in Computational Chemistry series brings together leading authorities in the field to teach the newcomer and update the expert on topics centered around molecular modeling, such as computer-assisted molecular design (CAMD), quantum chemistry, molecular mechanics and dynamics, and quantitative structure-activity relationships (QSAR). This volume, like those prior to it, features chapters by experts in various fields of computational chemistry. Topics in Volume 28 include:
* Free-energy Calculations with Metadynamics
* Polarizable Force Fields for Biomolecular Modeling
* Modeling Protein Folding Pathways
* Assessing Structural Predictions of Protein-Protein Recognition
* Kinetic Monte Carlo Simulation of Electrochemical Systems
* Reactivity and Dynamics at Liquid Interfaces
Sommario
Preface xi
List of Contributors xv
Contributors to Previous Volumes xvii
1. Free-Energy Calculations with Metadynamics: Theory and Practice 1
Giovanni Bussi and Davide Branduardi
Introduction 1
Molecular Dynamics and Free-Energy Estimation 3
Molecular Dynamics 3
Free-Energy Landscapes 4
A Toy Model: Alanine Dipeptide 6
Biased Sampling 8
Adaptive Biasing with Metadynamics 9
Reweighting 12
Well-Tempered Metadynamics 12
Reweighting 14
Metadynamics How-To 14
The Choice of the CV(s) 15
The Width of the Deposited Gaussian Potential 17
The Deposition Rate of the Gaussian Potential 18
A First Test Run Using Gyration Radius 19
A Better Collective Variable: Phi Dihedral Angle 23
Well-Tempered Metadynamics Using Gyration Radius 24
Well-Tempered Metadynamics Using Dihedral Angle Phi 27
Advanced Collective Variables 28
Path-Based Collective Variables 30
Collective Variables Based on Dimensional Reduction Methods 32
Template-Based Collective Variables 34
Potential Energy as a Collective Variable 35
Improved Variants 36
Multiple Walkers Metadynamics 36
Replica Exchange Metadynamics 37
Bias Exchange Metadynamics 38
Adaptive Gaussians 39
Conclusion 41
Acknowledgments 42
Appendix A: Metadynamics Input Files with PLUMED 42
References 44
2. Polarizable Force Fields for Biomolecular Modeling 51
Yue Shi, Pengyu Ren, Michael Schnieders, and Jean-Philip
Piquemal
Introduction 51
Modeling Polarization Effects 52
Induced Dipole Models 52
Classic Drude Oscillators 54
Fluctuating Charges 54
Recent Developments 55
AMOEBA 55
SIBFA 57
NEMO 58
CHARMM-Drude 58
CHARMM-FQ 59
X-Pol 60
PFF 60
Applications 61
Water Simulations 61
Ion Solvation 62
Small Molecules 63
Proteins 64
Lipids 66
Continuum Solvents for Polarizable Biomolecular Solutes 66
Macromolecular X-ray Crystallography Refinement 67
Prediction of Organic Crystal Structure, Thermodynamics, and Solubility 70
Summary 71
Acknowledgment 71
References 72
3. Modeling Protein Folding Pathways 87
Clare-Louise Towse and Valerie Daggett
Introduction 87
Outline of this Chapter 90
Protein Simulation Methodology 90
Force Fields, Models and Solvation Approaches 90
Unfolding: The Reverse of Folding 97
Elevated Temperature Unfolding Simulations 100
Biological Relevance of Forced Unfolding 103
Biased or Restrained MD 108
Characterizing Different States 111
Protein Folding and Refolding 115
Folding in Families 118
Conclusions and Outlook 121
Acknowledgment 122
References 122
4. Assessing Structural Predictions of Protein-Protein Recognition: The CAPRI Experiment 137
Joël Janin, Shoshana J. Wodak, Marc F. Lensink, and Sameer Velankar
Introduction 137
Protein-Protein Docking 138
A Short History of Protein-Protein Docking 138
Major Current Algorithms 141
The CAPRI Experiment 144
Why Do Blind Predictions? 144
Organizing CAPRI 145
The CAPRI Targets 146
Creating a Community 149
Assessing Dockin
Info autore
Abby L. Parrill, PhD, is Professor of Chemistry in the Department of Chemistry at the University of Memphis, TN. Her research interests are in bioorganic chemistry, protein modeling and NMR Spectroscopy and rational ligand design and synthesis. In 2011, she was awarded the Distinguished Research Award by University of Memphis Alumni Association. She has given more than 100 presentations, more than 100 papers and books.
Kenny B. Lipkowitz, PhD, is a recently retired Professor of Chemistry from North Dakota State University.
Riassunto
The Reviews in Computational Chemistry series brings together leading authorities in the field to teach the newcomer and update the expert on topics centered around molecular modeling, such as computer-assisted molecular design (CAMD), quantum chemistry, molecular mechanics and dynamics, and quantitative structure-activity relationships (QSAR).
