商品簡介
Answering the need to facilitate quantum-chemical calculations of systems with thousands of atoms, Kazuo Kitaura and his coworkers developed the Fragment Molecular Orbital (FMO) method in 1999. Today, the FMO method can be applied to the study of whole proteins and protein–ligand interactions, and is extremely effective in calculating the properties of biological systems and molecular clusters.
Providing a unique and accessible approach, The Fragment Molecular Orbital Method: Practical Applications to Large Molecular Systems is for those researchers eager to obtain useful information from electronic structure calculations of large systems, and for those who wish to know what can be elucidated with the calculations at present and in the near future. The text emphasizes the practical aspects, with as little mathematical detail as possible and in language that is easy to understand.
The free modeling software Facio, in which FMO-related functions are implemented, is provided on the accompanying CD-ROM, which also provides input file samples, usage hints, annotated output from typical calculations, easy-to-follow tutorial material, and AppliGuide movies that show the sequence of mouse operations for data processing.
The book encourages readers to perform their own calculations — describing the features of the freely available FMO programs (GAMESS and ABINIT-MP) and reviewing many successful applications of the FMO method to practical problems. Filled with practical advice from the inventors of the method and from world-renowned contributors, this reference provides general scientists with the foundation required to use FMO computational methods in a wide range of biomolecular applications, including drug design, protein–ligand binding, enzyme reactivity, and light-driven processes.
Developers interested in extending FMO capabilities or in advancing their own methods will find sufficient information and mathematical detail to encourage method development.
目次
Editors
Contributors
Chapter 1: Introduction; Kazuo Kitaura and Dmitri G. Fedorov
Chapter 2: Theoretical Background of the Fragment Molecular Orbital (Fmo) Method and Its Implementation in GAMESS; Dmitri G. Fedorov and Kazuo Kitaura
Chapter 3: Developments of FMO Methodology and Graphical User Interface in ABINIT-MP; Tatsuya Nakano, Yuji Mochizuki, Akifumi Kato, Kaori Fukuzawa, Takeshi Ishikawa, Shinji Amari, Ikuo Kurisaki, and Shigenori Tanaka
Chapter 4: Excited States of Photoactive Proteins by Configuration Interaction Studies; Yuji Mochizuki, Tatsuya Nakano, Naoki Taguchi, and Shigenori Tanaka
Chapter 5: The Fragment Molecular Orbital–Based Time-Dependent Density Functional Theory for Excited States in Large Systems; Mahito Chiba, Dmitri G. Fedorov, and Kazuo Kitaura
Chapter 6: FMO-MD: An Ab Initio-Based Molecular Dynamics of Large Systems; Yuto Komeiji
Chapter 7: Application of the FMO Method to Specific Molecular Recognition of Biomacromolecules; Kaori Fukuzawa, Yuji Mochizuki, Tatsuya Nakano, and Shigenori Tanaka
Chapter 8: Detailed Electronic Structure Studies Revealing the Nature of Protein–Ligand Binding; Isao Nakanishi, Dmitri G. Fedorov, and Kazuo Kitaura
Chapter 9: How Does the FMO Method Help in Studying Viruses and Their Binding to Receptors?; Toshihiko Sawada, Tomohiro Hashimoto, Hiroaki Tokiwa, Tohru Suzuki, Hirofumi Nakano, Hideharu Ishida, Makoto Kiso, and Yasuo Suzuki
Chapter 10: FMO as a Tool for Structure-Based Drug Design; Tomonaga Ozawa, Kosuke Okazaki, and Motohiro Nishio
Chapter 11: Modeling a Protein Environment in an Enzymatic Catalysis: A Case Study of the Chorismate Mutase Reaction; Toyokazu Ishida
Index
