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COVID-19 has brought us extensive research databases in the fields of biophysics, biology, and bioinformatics. To extract valuable structural bioinformatic information of SARS-CoV-2 structural and nonstructural proteins, it is necessary to work with large-scale datasets of molecular dynamics (MD) trajectories that need to be optimized. This monograph serves as a comprehensive guide to optimization-based MD studies of the molecular structures of SARS-CoV-2 proteins and RNA. The book begins by performing local optimization, taking into account the three-body movement and optimizing the noncovalent bonds of each molecular structure. The optimized structures reach a transition state that offers the best stability and lowest energy. The optimization process utilizes a hybrid strategy that combines mathematical optimization with various local search algorithms. This approach significantly reduces data volume while eliminating irrelevant bioinformatics data. To gain a thorough understanding of molecular stability and the mechanism of action, it is essential to consider not only static NMR, X-ray, or cryo-EM structures but also dynamic information obtained through MD or Quantum Mechanics/Molecular Mechanics (QM/MM) simulations. These simulations capture the internal motions and dynamic processes of molecules. Furthermore, for each protein, the structural bioinformatics obtained from the optimized structure is validated by analyzing large-scale MD trajectory databases, which are openly and freely available online. The analysis includes key structural bioinformatics aspects such as salt bridge electrostatic interactions, hydrogen bonds, van der Waals interactions, and hydrophobic interactions specific to each SARS-CoV-2 molecular structure. The book also delves into discussions on drugs, vaccines, and the origins of the virus. Additionally, pandemic mathematical models, including those incorporating time delays, are explored. This book is particularly valuable for professionals working in practical computing roles within computational biochemistry, computational biophysics, optimization and molecular dynamics, structural bioinformatics, biological mathematics, and related fields. It serves as an accessible introduction to these disciplines and is also an excellent teaching resource for students.

Biomolecules. --- Physical biochemistry. --- Macromolecules. --- Molecular biology. --- Biophysics. --- Proteins. --- Bioinformatics. --- Structural Biology. --- Molecular Biology. --- Molecular Biophysics. --- Protein Biochemistry.

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The chapters in this book are written by a team of well-reputed international researchers. The objective is to provide advanced and updated information related to protein-protein interactions. I hope the methods, resources and approaches described here will enhance the available knowledge of the reader significantly.

Protein-protein interactions. --- Interactions, Protein-protein --- PPIs (Protein-protein interactions) --- Protein interactions --- Interactomes --- Molecular association --- Life Sciences --- Immunology and Microbiology --- Structural Biology --- Proteomics

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This book focuses on the current status of our understanding of RNA, a key biological molecule. The various RNAs covered are messenger RNA, ribosomal RNA, transfer RNA, noncoding RNAs, modified nucleosides, and RNA enzymes. The different chapters detail methods to investigate RNA structure and function, the chemistry of modified RNAs, and the latest advances in our understanding of the vast array of biological processes in which RNA is involved. RNA, in one form or another, touches almost everything in a cell. RNA has both structural and catalytic properties. RNA fulfills a broad range of functions. These molecules are no longer seen as passive elements transferring the genetic information from DNA into proteins but regulate the activity of genes during development, cellular differentiation, and changing environments. RNAs are involved in various aspects of cell physiology and disease development. Discoveries of RNA with unexpected diverse functions in healthy and diseased cells, such as the role of RNA as both the source and countermeasure to cancer or severe viral infection, stimulate new trends, passion, and solutions for molecular medicine. In this book, fundamental questions about the biochemical and genetic importance of RNA, how mRNAs are generated and used to produce proteins, how noncoding and catalytic RNAs mediate key cellular processes, how to determine RNA structure and how to apply RNA in treatment of diseases. This book is an essential resource for researches in academia and industry contributing to the development of new RNA therapeutics. The book is geared toward scientists from the graduate level on up and particularly appeals to active investigators in RNA biology, molecular biology, and biochemistry.

RNA --- Structure --- Biomolecules. --- Physical biochemistry. --- Macromolecules. --- Biochemistry. --- Medical genetics. --- Cytology. --- Genetics. --- Structural Biology. --- Medical Genetics. --- Cell Biology. --- Genetics and Genomics. --- Piwi-Interacting RNA. --- RNA, Untranslated

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Biological Phenomena --- Biophysics --- Molecular biology --- Biologie moléculaire --- Biophysique --- Periodicals. --- Periodicals --- Périodiques --- Biological Phenomena. --- Biophysics. --- Biological physics --- Mechanobiology --- Biologic Phenomena --- Biological Phenomenon --- Biological Process --- Phenomena, Biological --- Biological Processes --- Phenomena, Biologic --- Phenomenon, Biological --- Process, Biological --- Processes, Biological --- molecular biosciences --- cells --- molecular biology --- quantitative biology --- Biology --- Medical sciences --- Physics --- Biology - General --- molecular biology --- biochemistry --- structural biology --- molecular therapeutics --- molecular modeling

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This book provides a unique, comprehensive, and up-to-date overview of the various NADPH oxidases and narrates the history of their discovery, biochemical characteristics, genetics, molecular structure, and multiple functions in health and disease. It covers the subject in a manner that serves both the expert and the novice researcher in the field. The book starts with an overview of the major milestones in the discovery of the archetypical NADPH oxidase, known as cytochrome b558, and its cytosolic regulators. This is followed by personal recollections by pioneers of the field, descriptions of the work of the major figures of the past by their followers, and a rendering of the history of the discovery of the Nox family. The central section of the book consists of chapters devoted specifically to an in depth description of the individual members of the Nox family, and is followed by chapters focused on the modulators of their function. A subsequent section comprises chapters dealing with methodologies of Nox research, interaction with other proteins, and Nox inhibitors. A distinct section of the book deals with non-mammalian Noxs, from amoeba to zebrafish. Subsequent chapters focus on Nox structure, a field in which extraordinary progress was made in recent years. The volume ends with chapters on Chronic Granulomatous Disease, the consequence of Nox loss-of-function, and its treatment by gene therapy. The coda is a crystal ball perspective of the hopes for the clinical translation of basic Nox research. Written for biochemists, cell biologists, molecular biologists, and clinicians, this book is aimed at both senior scientists and young investigators in the field.

Cytology. --- Stress (Physiology). --- Biomolecules. --- Physical biochemistry. --- Macromolecules. --- Diseases. --- Proteins. --- Cellular Stress. --- Structural Biology. --- Mechanisms of Disease. --- Protein Biochemistry. --- Proteids --- Biomolecules --- Polypeptides --- Proteomics --- Human beings --- Illness --- Illnesses --- Morbidity --- Sickness --- Sicknesses --- Medicine --- Epidemiology --- Health --- Pathology --- Sick --- Molecules --- Supramolecular chemistry --- Biophysical chemistry --- Biochemistry --- Physical organic chemistry --- Biological molecules --- Molecular biology --- Physiological stress --- Tension (Physiology) --- Adaptation (Biology) --- Cell biology --- Cellular biology --- Biology --- Cells --- Diseases