Recent Advances of the Fragment Molecular Orbital Method : Enhanced Performance and Applicability / edited by Yuji Mochizuki, Shigenori Tanaka, Kaori Fukuzawa.

Format:

Book

Contributor:

Mochizuki, Yuji, editor.

Tanaka, Shigenori, editor.

Fukuzawa, Kaori, editor.

SpringerLink (Online service)

Language:

English

Subjects (All):

Chemistry, Physical and theoretical.

Pharmacy.

Pharmaceutical technology.

Theoretical and Computational Chemistry.

Pharmaceutical Sciences/Technology.

Physical Chemistry.

Local Subjects:

Theoretical and Computational Chemistry.

Pharmacy.

Pharmaceutical Sciences/Technology.

Physical Chemistry.

Physical Description:

1 online resource (XI, 616 pages 269 illustrations, 231 illustrations in color.)

Edition:

First edition 2021.

Contained In:

Springer Nature eBook

Place of Publication:

Singapore : Springer Singapore : Imprint: Springer, 2021.

System Details:

text file PDF

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.

Contents:

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.

Other Format:

Printed edition:

ISBN:

9789811592355

Access Restriction:

Restricted for use by site license.