Optimization Based Molecular Dynamics Studies Of Sars Cov 2 Molecular Structures

Optimization-based Molecular Dynamics Studies of SARS-CoV-2 Molecular Structures

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.

Molecular Studies of COVID-19 Chemistry

Tea in Health and Disease Prevention

While there is a nearly universal agreement that drinking tea can benefit health, information on the benefits or adverse effects of drinking tea is scattered, leaving definitive answers difficult to ascertain. Tea in Health and Disease Prevention, Second Edition, once again addresses this problem, bringing together all the latest and most relevant information on tea and its health effects into one comprehensive resource. This book covers compounds in black, green, and white teas and explores their health implications, first more generally, then in terms of specific organ systems and diseases. With over 75% brand new content, this fully reorganized, updated edition covers a wider range of tea varieties and beneficial compounds found in tea, such as epigallocatechin gallate and antioxidants.Tea in Health and Disease Prevention, Second Edition, is an organized, efficient resource that will help readers find quick answers to questions and will help inspire further studies for those interested in tea research. This is a must-have reference for researchers in food science and nutrition, as well as nutritionists and dieticians. - Covers and compares features, benefits, and potential negative effects of the most important types of tea, including green, black, and white - Identifies therapeutic benefits of teas for new product development - Offers a "one stop shop" for research in this area, compiling both foundational and cutting-edge topics into one resource - Includes a dictionary of key terms, other health effects of tea or extracts, and a summary point section within each chapter for a quick reference