Reviews in Computational Chemistry, Reviews in Computational Chemistry, Volume 17 / Edition 1by Kenny B. Lipkowitz
This volume, like those prior to it, features chapters by experts in various fields of computational chemistry. Two chapters focus on molecular docking, one of which relates to drug discovery and cheminformatics and the other to proteomics. In addition, this volume contains tutorials on spin-orbit coupling and cellular automata modeling, as well as an extensive… See more details below
This volume, like those prior to it, features chapters by experts in various fields of computational chemistry. Two chapters focus on molecular docking, one of which relates to drug discovery and cheminformatics and the other to proteomics. In addition, this volume contains tutorials on spin-orbit coupling and cellular automata modeling, as well as an extensive bibliography of computational chemistry books.
FROM REVIEWS OF THE SERIES "Reviews in Computational Chemistry remains the most valuable reference to methods and techniques in computational chemistry."-JOURNAL OF MOLECULAR GRAPHICS AND MODELLING
"One cannot generally do better than to try to find an appropriate article in the highly successful Reviews in Computational Chemistry. The basic philosophy of the editors seems to be to help the authors produce chapters that are complete, accurate, clear, and accessible to experimentalists (in particular) and other nonspecialists (in general)."-JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
Table of Contents
1. Small Molecule Docking and Scoring (Ingo Muegge and Matthias Rarey).
Algorithms for Molecular Docking.
Appendix. Books Published on the Topics of Computational Chemistry (Kenny B. Lipkowitz and Donald B. Boyd).
Computers in Chemistry.
Artificial Intelligence and Chemometrics.
Crystallography, Spectroscopy, and Thermochemistry.
Fundamentals of Quantum Theory.
Applied Quantum Chemistry.
Crystals, Polymers, and Materials.
Selected Series and Proceedings from Long-Running Conferences.
Molecular Design and Quantitative Structure-Activity Relationships.
Graph Theory in Chemistry.
The Docking Problem.
Placing Fragments and Rigid Molecules.
Flexible Ligand Docking.
Handling Protein Flexibility.
Docking of Combinatorial Libraries.
Shape and Chemical Complementary Scores.
Force Field Scoring.
Empirical Scoring Functions.
Knowledge-Based Scoring Functions.
Comparing Scoring Functions in Docking Experiments: Consensus Scoring.
From Molecular Docking to Virtual Screening.
Protein Data Preparation.
Ligand Database Preparation.
Docking as a Virtual Screening Tool.
Docking as a Ligand Design Tool.
2. Protein-Protein Docking (Lutz P. Ehrlich and Rebecca C. Wade).
Why This Topic?
Protein-Protein Binding Data.
Challenges for Computational Docking Studies.
Computational Approaches to the Docking Problem.
Docking = Sampling + Scoring.
Estimating the Extent of Conformational Change upon Binding.
Flexible Docking with Side-Chain Flexibility.
Flexible Docking with Full Flexibility.
3. Spin-Orbit Coupling in Molecules (Christel M. Marian).
What It Is All About.
The Fourth Electronic Degree of Freedom.
The Stern-Gerlach Experiment.
Spin Is a Quantum Effect.
Orbital Angular Momentum.
General Angular Momenta.
Spin Angular Momentum.
Full One- and Two-Electron Spin-Orbit Operators.
Valence-Only Spin-Orbit Hamiltonians.
Effective One-Electron Spin-Orbit Hamiltonians.
Transformation Properties of the Wave Function.
Transformation Properties of the Hamiltonian.
Evaluation of Spin-Orbit Integrals.
Perturbational Approaches to Spin-Orbit Coupling.
Comparison of Fine-Structure Splittings with Experiment.
First-Order Spin-Orbit Splitting.
Second-Order Spin-Orbit Splitting.
Summary and Outlook.
4. Cellular Automata Models of Aqueous Solution Systems (Lemont B. Kier, Chao-Kun Cheng, and Paul G. Seybold).
The General Structure.
Movement (Transition) Rules.
Collection of Data.
Aqueous Solution Systems.
Water as a System.
The Molecular Model.
Significance of the Rules.
Studies of Water and Solution Phenomena.
A Cellular Automata Model of Water.
The Hydrophobic Effect.
Immiscible Liquids and Partitioning.
Solution Kinetic Models.
Kinetic and Thermodynamic Reaction Control.
An Anticipatory Model.
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