Recent advances of the fragment molecular orbital method : enhanced performance and applicability / Yuji Mochizuki, Shigenori Tanaka, Kaori Fukuzawa, editors.
Mochizuki, Yuji, editor.; Tanaka, Shigenori, editor.; Fukuzawa, Kaori, editor.
2021
QD461
Available Online

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Title
Recent advances of the fragment molecular orbital method : enhanced performance and applicability / Yuji Mochizuki, Shigenori Tanaka, Kaori Fukuzawa, editors.
ISBN
9789811592355 (electronic bk.)
9811592357 (electronic bk.)
9811592349
9789811592348
DOI
https://doi.org/10.1007/978-981-15-9235-5
Publication Details
Singapore : Springer, 2021.
Language
English
Description
1 online resource
Item Number
10.1007/978-981-15-9235-5 doi
Call Number
QD461
Dewey Decimal Classification
541/.28
Summary
This book covers recent advances of the fragment molecular orbital (FMO) method, consisting of 5 parts and a total of 30 chapters written by FMO experts. The FMO method is a promising way to calculate large-scale molecular systems such as proteins in a quantum mechanical framework. The highly efficient parallelism deserves being considered the principal advantage of FMO calculations. Additionally, the FMO method can be employed as an analysis tool by using the inter-fragment (pairwise) interaction energies, among others, and this feature has been utilized well in biophysical and pharmaceutical chemistry. In recent years, the methodological developments of FMO have been remarkable, and both reliability and applicability have been enhanced, in particular, for non-bio problems. The current trend of the parallel computing facility is of the many-core type, and adaptation to modern computer environments has been explored as well. In this book, a historical review of FMO and comparison to other methods are provided in Part I (two chapters) and major FMO programs (GAMESS-US, ABINIT-MP, PAICS and OpenFMO) are described in Part II (four chapters). dedicated to pharmaceutical activities (twelve chapters). A variety of new applications with methodological breakthroughs are introduced in Part IV (six chapters). Finally, computer and information science-oriented topics including massively parallel computation and machine learning are addressed in Part V (six chapters). Many color figures and illustrations are included. Readers can refer to this book in its entirety as a practical textbook of the FMO method or read only the chapters of greatest interest to them.
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Access limited to authorized users.
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text file
PDF
Source of Description
Online resource; title from PDF title page (SpringerLink, viewed March 3, 2021).
Added Author
Mochizuki, Yuji, editor.
Tanaka, Shigenori, editor.
Fukuzawa, Kaori, editor.
Available in Other Form
Print version: 9789811592348
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Part 1: Positioning of FMO
Fragment molecular orbital method as cluster expansion
Comparison of various fragmentation methods for quantum chemical calculations of large molecular systems
Part 2: Programs
Recent development of the fragment molecular orbital method in GAMESS
The ABINIT-MP program
PAICS: Development of An Open-Source Software of Fragment Molecular Orbital Method for Biomolecule
Open-Architecture Program of Fragment Molecular Orbital Method for Massive Parallel Computing (OpenFMO) with GPU Acceleration
Part 3: Pharmaceutical activities
How to perform FMO calculation in Drug Discovery
FMO drug design consortium
Development of an automated FMO calculation protocol to construction of FMO database
Application of FMO to ligand design: SBDD, FBDD, and protein-protein interaction
Drug Discovery Screening by Combination of X-ray Crystal Structure Analysis and FMO Calculation
Cooperative study combining X-ray crystal structure analysis and FMO calculation: Interaction analysis of FABP4 inhibitors
Application of FMO for protein-ligand binding affinity prediction
Recent Advances of In Silico Drug Discovery: Integrated Systems of Informatics and Simulation
Pharmaceutical Industry
Academia Cooperation
Elucidating the efficacy of clinical drugs using FMO
Application of Fragment Molecular Orbital Calculations to Functional Analysis of Enzymes
AnalysisFMO toolkit: A PyMOL plugin for 3D-visualization of interaction energies in proteins (3D-VIEP) calculated by the FMO method
Part 4: New methods and applications
FMO interfaced with Molecular Dynamics simulation
Linear Combination of Molecular Orbitals of Fragments (FMO-LCMO) Method: Its Application to Charge Transfer Studies
Modeling of solid and surface
Development of the analytic second derivatives for the fragment molecular orbital method
The FMO-DFTB Method
Self-consistent treatment of solvation structure with electronic structure based on 3D-RISM theory
New methodology and framework
New methodology and framework Information science-assisted analysis of FMO results for Drug Design
Extension to multiscale simulations
FMO-based investigations of excited-state dynamics in molecular aggregates
Application of the fragment molecular orbital method to organic charge transport materials in xerography: a feasibility study and a charge mobility analysis
Group molecular orbital method and Python-based programming approach
Multi-level parallelization of the fragment molecular orbital method in GAMESS.

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