Recent Advances of the Fragment Molecular Orbital Method
Recent Advances of the Fragment Molecular Orbital Method

Author: Yuji Mochizuki

Publisher: Springer Nature

Published: 2021-01-04

Total Pages: 606

ISBN-13: 9811592357

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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.

The Fragment Molecular Orbital Method
The Fragment Molecular Orbital Method

Author: Dmitri Fedorov

Publisher: CRC Press

Published: 2009-05-14

Total Pages: 304

ISBN-13: 1420078496

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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 propertie

Complete Guide To The Fragment Molecular Orbital Method In Gamess: From One Atom To A Million, At Your Service
Complete Guide To The Fragment Molecular Orbital Method In Gamess: From One Atom To A Million, At Your Service

Author: Dmitri G Fedorov

Publisher: World Scientific

Published: 2023-02-17

Total Pages: 326

ISBN-13: 9811263647

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The fragment molecular orbital (FMO) method is a fast linear-scaling quantum-mechanical method employed by chemists and physicists all over the world. It provides a wealth of properties of fragments from quantum-chemical calculations, a bottomless treasure pit for data mining and machine learning. However, there is no user-friendly description of its usage in the widely employed quantum-chemical open-source software GAMESS, nor is there any book covering the usage of GAMESS in general. This leaves very many interested users to their own devices to get through a variety of problems with very cryptic descriptions of keywords in the program manual and no guide whatsoever as to what options should be set for particular scientific tasks. This book is the panacea to many frustrations.The main focus of the book is to build a solid bridge connecting FMO users to GAMESS, by giving a helpful introduction of various FMO methods as needed for particular problems found in computational chemistry, and describing in detail how to do these simulations and understand the results from the output of the program. The book also covers parallelization strategies for attaining high parallel efficiency in massively parallel computations, and provides means to analyze performance and design a solution for overcoming performance bottlenecks. A special section is devoted to dealing with problems in executing GAMESS, arising from computational environment and user errors. Finally, 14 carefully selected types of applications are discussed in detail, describing the input keywords and explaining where to find the main results in the text-based output.

Computational Drug Discovery
Computational Drug Discovery

Author: Vasanthanathan Poongavanam

Publisher: John Wiley & Sons

Published: 2024-01-19

Total Pages: 882

ISBN-13: 3527840737

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Computational Drug Discovery A comprehensive resource that explains a wide array of computational technologies and methods driving innovation in drug discovery Computational Drug Discovery: Methods and Applications (2 volume set) covers a wide range of cutting-edge computational technologies and computational chemistry methods that are transforming drug discovery. The book delves into recent advances, particularly focusing on artificial intelligence (AI) and its application for protein structure prediction, AI-enabled virtual screening, and generative modeling for compound design. Additionally, it covers key technological advancements in computing such as quantum and cloud computing that are driving innovations in drug discovery. Furthermore, dedicated chapters that addresses the recent trends in the field of computer aided drug design, including ultra-large-scale virtual screening for hit identification, computational strategies for designing new therapeutic modalities like PROTACs and covalent inhibitors that target residues beyond cysteine are also presented. To offer the most up-to-date information on computational methods utilized in computational drug discovery, it covers chapters highlighting the use of molecular dynamics and other related methods, application of QM and QM/MM methods in computational drug design, and techniques for navigating and visualizing the chemical space, as well as leveraging big data to drive drug discovery efforts. The book is thoughtfully organized into eight thematic sections, each focusing on a specific computational method or technology applied to drug discovery. Authored by renowned experts from academia, pharmaceutical industry, and major drug discovery software providers, it offers an overview of the latest advances in computational drug discovery. Key topics covered in the book include: Application of molecular dynamics simulations and related approaches in drug discovery The application of QM, hybrid approaches such as QM/MM, and fragment molecular orbital framework for understanding protein-ligand interactions Adoption of artificial intelligence in pre-clinical drug discovery, encompassing protein structure prediction, generative modeling for de novo design, and virtual screening. Techniques for navigating and visualizing the chemical space, along with harnessing big data to drive drug discovery efforts. Methods for performing ultra-large-scale virtual screening for hit identification. Computational strategies for designing new therapeutic models, including PROTACs and molecular glues. In silico ADMET approaches for predicting a variety of pharmacokinetic and physicochemical endpoints. The role of computing technologies like quantum computing and cloud computing in accelerating drug discovery This book will provide readers an overview of the latest advancements in computational drug discovery and serve as a valuable resource for professionals engaged in drug discovery.

Fragmentation: Toward Accurate Calculations on Complex Molecular Systems
Fragmentation: Toward Accurate Calculations on Complex Molecular Systems

Author: Mark S. Gordon

Publisher: John Wiley & Sons

Published: 2017-10-23

Total Pages: 376

ISBN-13: 1119129249

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Fragmentation: Toward Accurate Calculations on Complex Molecular Systems introduces the reader to the broad array of fragmentation and embedding methods that are currently available or under development to facilitate accurate calculations on large, complex systems such as proteins, polymers, liquids and nanoparticles. These methods work by subdividing a system into subunits, called fragments or subsystems or domains. Calculations are performed on each fragment and then the results are combined to predict properties for the whole system. Topics covered include: Fragmentation methods Embedding methods Explicitly correlated local electron correlation methods Fragment molecular orbital method Methods for treating large molecules This book is aimed at academic researchers who are interested in computational chemistry, computational biology, computational materials science and related fields, as well as graduate students in these fields.

Quantum Mechanics in Drug Discovery
Quantum Mechanics in Drug Discovery

Author: Alexander Heifetz

Publisher: Humana

Published: 2021-02-18

Total Pages: 360

ISBN-13: 9781071602843

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This volume looks at applications of quantum mechanical (QM) methods in drug discovery. The chapters in this book describe how QM approaches can be applied to address key drug discovery issues, such as characterizing protein-water-ligand and protein-protein interactions, providing estimates of binding affinities, determining ligand energies and bioactive conformations, refinement of molecular geometries, scoring docked protein–ligand poses, describing molecular similarity, structure–activity-relationship (SAR) analysis, and ADMET prediction. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary software and tools, step-by-step, readily reproducible modeling protocols, and tips on troubleshooting and avoiding known pitfalls. Cutting-edge and unique, Quantum Mechanics in Drug Discovery is a valuable resource for structural and molecular biologists, computational and medicinal chemists, pharmacologists, and drug designers.

Organic Solar Cells
Organic Solar Cells

Author: Masahiro Hiramoto

Publisher: Springer Nature

Published: 2020-12-16

Total Pages: 271

ISBN-13: 981159113X

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This book focuses on the essential scientific ideas and breakthroughs in the last three decades for organic solar cells that have realized practical applications. The motivation for publishing this book is to explain how those essential ideas have arisen and to provide a foundation for future progress by target readers—students, novices in the field, and scientists with expertise. The main topics covered in the book include the fundamental principles and history of organic solar cells, blended junction, nanostructure control, photocurrent generation, photovoltage generation, doping, practical organic solar cells, and possible ideas for the future. The editors enthusiastically anticipate the vigorous development of the field of organic solar cells by young scientists of the next generation.

Molecular Dynamics
Molecular Dynamics

Author: Lichang Wang

Publisher: BoD – Books on Demand

Published: 2012-04-05

Total Pages: 440

ISBN-13: 9535104438

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Molecular Dynamics is a two-volume compendium of the ever-growing applications of molecular dynamics simulations to solve a wider range of scientific and engineering challenges. The contents illustrate the rapid progress on molecular dynamics simulations in many fields of science and technology, such as nanotechnology, energy research, and biology, due to the advances of new dynamics theories and the extraordinary power of today's computers. This first book begins with a general description of underlying theories of molecular dynamics simulations and provides extensive coverage of molecular dynamics simulations in nanotechnology and energy. Coverage of this book includes: Recent advances of molecular dynamics theory Formation and evolution of nanoparticles of up to 106 atoms Diffusion and dissociation of gas and liquid molecules on silicon, metal, or metal organic frameworks Conductivity of ionic species in solid oxides Ion solvation in liquid mixtures Nuclear structures

Managing the Drug Discovery Process
Managing the Drug Discovery Process

Author: Susan Miller

Publisher: Elsevier

Published: 2023-03-09

Total Pages: 684

ISBN-13: 0128243058

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Managing the Drug Discovery Process, Second Edition thoroughly examines the current state of pharmaceutical research and development by providing experienced perspectives on biomedical research, drug hunting and innovation, including the requisite educational paths that enable students to chart a career path in this field. The book also considers the interplay of stakeholders, consumers, and drug firms with respect to a myriad of factors. Since drug research can be a high-risk, high-payoff industry, it is important to students and researchers to understand how to effectively and strategically manage both their careers and the drug discovery process. This new edition takes a closer look at the challenges and opportunities for new medicines and examines not only the current research milieu that will deliver novel therapies, but also how the latest discoveries can be deployed to ensure a robust healthcare and pharmacoeconomic future. All chapters have been revised and expanded with new discussions on remarkable advances including CRISPR and the latest gene therapies, RNA-based technologies being deployed as vaccines as well as therapeutics, checkpoint inhibitors and CAR-T approaches that cure cancer, diagnostics and medical devices, entrepreneurship, and AI. Written in an engaging manner and including memorable insights, this book is aimed at anyone interested in helping to save countless more lives through science. A valuable and compelling resource, this is a must-read for all students, educators, practitioners, and researchers at large—indeed, anyone who touches this critical sphere of global impact—in and around academia and the biotechnology/pharmaceutical industry. - Considers drug discovery in multiple R&D venues - big pharma, large biotech, start-up ventures, academia, and nonprofit research institutes - with a clear description of the degrees and training that will prepare students well for a career in this arena - Analyzes the organization of pharmaceutical R&D, taking into account human resources considerations like recruitment and configuration, management of discovery and development processes, and the coordination of internal research within, and beyond, the organization, including outsourced work - Presents a consistent, well-connected, and logical dialogue that readers will find both comprehensive and approachable - Addresses new areas such as CRISPR gene editing technologies and RNA-based drugs and vaccines, personalized medicine and ethical and moral issues, AI/machine learning and other in silico approaches, as well as completely updating all chapters