The Fragment Molecular Orbital Method: Practical Applications to Large Molecular Systems

by Fedorov; Dmitri

• ISBN13: 9781420078480
• ISBN10: 1420078488
• Edition: 1st
• Format: Hardcover
• Copyright: 2009-05-14
• Publisher: CRC Press

Summary

Considered a promising alternative for modeling large molecules of biochemical interest, the fragment molecular orbital method (FMO) shows great promise when applied to any number of biochemical problems, especially in drug design, protein-ligand binding, enzyme reactivity, and light-driven processes. This handbook, written by the inventors of the process, makes FMO accessible. The authors present the necessary foundation material in a way that the general scientist will understand and demonstrate applications to biochemical studies that emphasize practical aspects of performing actual simulations. The text pays some attention to FMO-enabled software. An attached CD-ROM will allow scientists to perform calculations.

Table of Contents

Editors	p. vii
Contributors	p. ix
Introduction	p. 1
Theoretical Background of the Fragment Molecular Orbital (FMO) Method and Its Implementation in Gamess	p. 5
Developments of FMO Methodology and Graphical User Interface in Abinit-Mp	p. 37
Excited States of Photoactive Proteins by Configuration Interaction Studies	p. 63
The Fragment Molecular Orbital-Based Time-Dependent Density Functional Theory for Excited States in Large Systems	p. 91
FMO-MD: An Ab Initio-Based Molecular Dynamics of Large Systems	p. 119
Application of the FMO Method to Specific Molecular Recognition of Biomacromolecules	p. 133
Detailed Electronic Structure Studies Revealing the Nature of Protein-Ligand Binding	p. 171
How Does the FMO Method Help in Studying Viruses and Their Binding to Receptors?	p. 193
FMO as a Tool for Structure-Based Drug Design	p. 217
Modeling a Protein Environment in an Enzymatic Catalysis: A Case Study of the Chorismate Mutase Reaction	p. 245
Index	p. 269
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