Download or read book Optimization based Molecular Dynamics Studies of SARS CoV 2 Molecular Structures written by Jiapu Zhang and published by Springer Nature. This book was released on 2023-10-16 with total page 956 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Download or read book Molecular Studies of COVID 19 Chemistry written by Emilia Pedone and published by Frontiers Media SA. This book was released on 2021-10-20 with total page 251 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book In Silico Generation of Novel Ligands for the Inhibition of SARS CoV 2 Main Protease 3CLpro Using Deep Learning written by Prejwal Prabhakaran and published by . This book was released on 2023 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Abstract: The recent emergence of novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causing the coronavirus disease (COVID-19) has become a global public health crisis, and a crucial need exists for rapid identification and development of novel therapeutic interventions. In this study, a recurrent neural network (RNN) is trained and optimized to produce novel ligands that could serve as potential inhibitors to the SARS-CoV-2 viral protease: 3 chymotrypsin-like protease (3CLpro). Structure-based virtual screening was performed through molecular docking, ADMET profiling, and predictions of various molecular properties were done to evaluate the toxicity and drug-likeness of the generated novel ligands. The properties of the generated ligands were also compared with current drugs under various phases of clinical trials to assess the efficacy of the novel ligands. Twenty novel ligands were selected that exhibited good drug-likeness properties, with most ligands conforming to Lipinski's rule of 5, high binding affinity (highest binding affinity: −9.4 kcal/mol), and promising ADMET profile. Additionally, the generated ligands complexed with 3CLpro were found to be stable based on the results of molecular dynamics simulation studies conducted over a 100 ns period. Overall, the findings offer a promising avenue for the rapid identification and development of effective therapeutic interventions to treat COVID-19
Download or read book Molecular Docking and Molecular Dynamics written by Amalia Stefaniu and published by BoD – Books on Demand. This book was released on 2019-12-18 with total page 102 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book clearly explains the principles of in silico tools of molecular docking and molecular dynamics. It provides examples of algorithms and procedures proposed by different software programs for visualizing and identifying potential interactions in complexes of biochemical interest. The book is structured in six chapters, each of which discusses different molecular simulation methodologies and provides concrete examples of complexes interactions. In each chapter authors give an overview of the treated subject, a description of the methodologies used, and a discussion of the results. The authors describe computational ways to achieve a rational design of bioactive compounds with various therapeutic applications, including antitumoral agents, antitubercular drugs, nonsteroidal anti-inflammatory drugs, and radiopharmaceuticals.
Download or read book QSAR written by Hugo Kubinyi and published by John Wiley & Sons. This book was released on 2008-07-11 with total page 252 pages. Available in PDF, EPUB and Kindle. Book excerpt: Finding the new remedy for a certain disease: an inspired goal. QSAR, an invaluable tool in drug design, aids scientists to attain this aim. This book is a long-awaited comprehensive text to QSAR and related approaches. It provides a practice-oriented introduction to the theory, methods and analyses for QSAR relationships, including modelling-based and 3D approaches. Hugo Kubinyi is a leading expert in QSAR. Readers will benefit from the author's 20 years of practical experience, from his careful calculations and recalculations of thousands of QSAR equations. Among the topics covered are: - physiocochemical parameters - quantitative models - statistical methods - Hansch analysis - Free Wilson analysis - 3D-QSAR approaches The book can readily be used as a textbook due to its high didactic value and numerous examples (over 200 equations and 1100 references).
Download or read book Advances in Protein Molecular and Structural Biology Methods written by Timir Tripathi and published by Academic Press. This book was released on 2022-01-14 with total page 716 pages. Available in PDF, EPUB and Kindle. Book excerpt: Advances in Protein Molecular and Structural Biology Methods offers a complete overview of the latest tools and methods applicable to the study of proteins at the molecular and structural level. The book begins with sections exploring tools to optimize recombinant protein expression and biophysical techniques such as fluorescence spectroscopy, NMR, mass spectrometry, cryo-electron microscopy, and X-ray crystallography. It then moves towards computational approaches, considering structural bioinformatics, molecular dynamics simulations, and deep machine learning technologies. The book also covers methods applied to intrinsically disordered proteins (IDPs)followed by chapters on protein interaction networks, protein function, and protein design and engineering. It provides researchers with an extensive toolkit of methods and techniques to draw from when conducting their own experimental work, taking them from foundational concepts to practical application. Presents a thorough overview of the latest and emerging methods and technologies for protein study Explores biophysical techniques, including nuclear magnetic resonance, X-ray crystallography, and cryo-electron microscopy Includes computational and machine learning methods Features a section dedicated to tools and techniques specific to studying intrinsically disordered proteins
Download or read book STD Interchange written by and published by . This book was released on 1984 with total page 40 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book COVID 19 written by Moones Rahmandoust and published by Springer Nature. This book was released on 2021-08-13 with total page 275 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book highlights the overview of the COVID-19 pandemic from both the scientific and the social perspectives. The scientific part presents key facts of COVID-19, including the structure of the virus and the techniques for the diagnosis, treatment, and vaccine development against the disease, covering state-of-the-art findings and achievements worldwide. The social part is written by WHO professionals who worked on the frontier of the fight against the disease. It covers the global security situation during the pandemic, the WHO and governmental-level risk management measures, and the estimated impact that COVID-19 will eventually create on social life after it is globally controlled.
Download or read book Drug Discovery and Development written by Vishwanath Gaitonde and published by BoD – Books on Demand. This book was released on 2020-03-11 with total page 166 pages. Available in PDF, EPUB and Kindle. Book excerpt: The process of drug discovery and development is a complex multistage logistics project spanned over 10-15 years with an average budget exceeding 1 billion USD. Starting with target identification and synthesizing anywhere between 10k to 15k synthetic compounds to potentially obtain the final drug that reaches the market involves a complicated maze with multiple inter- and intra-operative fields. Topics described in this book emphasize the progresses in computational applications, pharmacokinetics advances, and molecular modeling developments. In addition the book also contains special topics describing target deorphaning in Mycobacterium tuberculosis, therapy treatment of some rare diseases, and developments in the pediatric drug discovery process.
Download or read book Docking Screens for Drug Discovery written by Walter Filgueira de Azevedo Jr. and published by Humana. This book was released on 2019-08-27 with total page 286 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book focuses on recent developments in docking simulations for target proteins with chapters on specific techniques or applications for docking simulations, including the major docking programs. Additionally, the volume explores the scoring functions developed for the analysis of docking results and to predict ligand-binding affinity as well as the importance of docking simulations for the initial stages of drug discovery. Written for the highly successful Methods in Molecular Biology series, this collection presents the kind of detail and key implementation advice to ensure successful results. Authoritative and practical, Docking Screens for Drug Discovery aims to serve those interested in molecular docking simulation and also in the application of these methodologies for drug discovery.
Download or read book Endemic Plants Experimental and Theoretical Insights Into Properties of Bioactive Metabolites With Therapeutic Potential written by Carolina Otero and published by Frontiers Media SA. This book was released on 2021-12-29 with total page 67 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Gayletter written by Gayletter and published by . This book was released on 2021-07-20 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Applied Big Data Analytics and Its Role in COVID 19 Research written by Zhao, Peng and published by IGI Global. This book was released on 2022-04-29 with total page 349 pages. Available in PDF, EPUB and Kindle. Book excerpt: There has been a multitude of studies focused on the COVID-19 pandemic across fields and disciplines as all sectors of life have had to adjust the way things are done and adapt to the constantly shifting environment. These studies are crucial as they provide support and perspectives on how things are changing and what needs to be done to stay afloat. Connecting COVID-19-related studies and big data analytics is crucial for the advancement of industrial applications and research areas. Applied Big Data Analytics and Its Role in COVID-19 Research introduces the most recent industrial applications and research topics on COVID-19 with big data analytics. Featuring coverage on a broad range of big data technologies such as data gathering, artificial intelligence, smart diagnostics, and mining mobility, this publication provides concrete examples and cases of usage of data-driven projects in COVID-19 research. This reference work is a vital resource for data scientists, technical managers, researchers, scholars, practitioners, academicians, instructors, and students.
Download or read book Molecular Dynamics Simulation of Nanocomposites using BIOVIA Materials Studio Lammps and Gromacs written by Sumit Sharma and published by Elsevier. This book was released on 2019-08-09 with total page 368 pages. Available in PDF, EPUB and Kindle. Book excerpt: Molecular Dynamics Simulation of Nanocomposites using BIOVIA Materials Studio, Lammps and Gromacs presents the three major software packages used for the molecular dynamics simulation of nanocomposites. The book explains, in detail, how to use each of these packages, also providing real-world examples that show when each should be used. The latter two of these are open-source codes which can be used for modeling at no cost. Several case studies how each software package is used to predict various properties of nanocomposites, including metal-matrix, polymer-matrix and ceramic-matrix based nanocomposites. Properties explored include mechanical, thermal, optical and electrical properties. This is the first book that explores methodologies for using Materials Studio, Lammps and Gromacs in the same place. It will be beneficial for students, researchers and scientists working in the field of molecular dynamics simulation. Gives a detailed explanation of basic commands and modules of Materials Studio, Lammps and Gromacs Shows how Materials Studio, Lammps and Gromacs predict mechanical, thermal, electrical and optical properties of nanocomposites Uses case studies to show which software should be used to solve a variety of nanoscale modeling problems
Download or read book Biomedical Innovations to Combat COVID 19 written by Sergio Rosales-Mendoza and published by Academic Press. This book was released on 2021-10-15 with total page 411 pages. Available in PDF, EPUB and Kindle. Book excerpt: Biomedical Innovations to Combat COVID-19 provides an updated overview on the development of vaccines, antiviral drugs and nanomaterials, and diagnostic methods for the fight against COVID-19. Perspectives on such technologies are identified, discussed, and enriched with figures for easy understanding and applicability. Furthermore, it contains basic aspects of virology, immunology, and antiviral drugs that are needed to fully appreciate these innovations. This book is split into four sections: introduction, presenting basic virologic and epidemiological aspects of COVID-19; vaccines against COVID-19, discussing their different types and applications used to develop them; diagnostic approaches for SARS-CoV-2, encompassing advanced sensing and microfluidic-based biosensors; and drug development and delivery, where antivirals based on nanomaterials or drugs are presented. It is a valuable source for virologists, biotechnologists, and members of biomedical field interested in learning more about how novel technologies can be applied to fasten the eradication of the COVID-19 and similar pandemics. Presents updated literature coverage summarizing the most relevant information on COVID-19 Written by experts from diverse scientific domains in order to provide readers with a thorough view on the subject Encompasses tables, figures and information trees especially developed for the book in order to condense and highlight key points for quick reference
Download or read book Electronic Structure Methods for Complex Materials written by Wai-Yim Ching and published by OUP Oxford. This book was released on 2012-05-17 with total page 328 pages. Available in PDF, EPUB and Kindle. Book excerpt: Density functional theory (DFT) has blossomed in the past few decades into a powerful tool that is used by experimentalists and theoreticians alike. This book highlights the extensive contributions that the DFT-based OLCAO method has made to progress in this field, and it demonstrates its competitiveness for performing ab initio calculations on large and complex models of practical systems. A brief historical account and introduction to the elements of the theory set the stage for discussions on semiconductors, insulators, crystalline metals and alloys, complex crystals, non-crystalline solids and liquids, microstructure containing systems and those containing impurities, defects, and surfaces, biomolecular systems, and the technique of ab initio core level spectroscopy calculation.
Download or read book Molecular Docking for Computer Aided Drug Design written by Mohane S. Coumar and published by Academic Press. This book was released on 2021-02-17 with total page 522 pages. Available in PDF, EPUB and Kindle. Book excerpt: Molecular Docking for Computer-Aided Drug Design: Fundamentals, Techniques, Resources and Applications offers in-depth coverage on the use of molecular docking for drug design. The book is divided into three main sections that cover basic techniques, tools, web servers and applications. It is an essential reference for students and researchers involved in drug design and discovery. Covers the latest information and state-of-the-art trends in structure-based drug design methodologies Includes case studies that complement learning Consolidates fundamental concepts and current practice of molecular docking into one convenient resource
