Download or read book Protein Design from in Silico to in Vivo written by Arnab Bula Chowdry and published by . This book was released on 2008 with total page 242 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Combining in Vivo and in Silico Screening for Protein Stability written by Nora Hisham Barakat and published by . This book was released on 2007 with total page 167 pages. Available in PDF, EPUB and Kindle. Book excerpt: In the in vivo 'chimeric' screen a target protein is expressed as a fusion protein with a DNA binding domain fused at the N-terminus and a transactivation domain at the C-terminus. This three-component fusion protein acts as a functional transcription factor for a reporter gene. If the central target protein is relatively unstable it is more flexible and thereby allows the DNA binding domain and the transactivation domain to achieve an optimal orientation for transcriptional activation. Conversely, if the central target protein is highly stable it is too rigid to allow the DNA binding domain and the transactivation domain to achieve the proper orientation for transcriptional activation and thus is a less efficient transcription factor.
Download or read book Combining in Vivo and in Silico Screening for Protein Stability written by and published by . This book was released on 2007 with total page 304 pages. Available in PDF, EPUB and Kindle. Book excerpt: In any protein design endeavor, thermal stability is an important issue. Increasing protein stability is currently one of the main goals of the field of protein design as well as the biomedical industry. It is important for developing stable protein-based therapeutics and ultimately enhances our understanding of the principles of protein folding. The overall goal of my project is to develop and combine in vivo and in silico screening and analysis to select stable proteins from a large combinatorial library of proteins. Our in vivo screening method is based solely on the stability of the test proteins, and is independent of protein function. In addition, the mutant variants obtained from the in vivo screen were further analyzed and screened in silico with the ORBIT protein design package. In the in vivo 'chimeric' screen a target protein is expressed as a fusion protein with a DNA binding domain fused at the N-terminus and a transactivation domain at the C-terminus. This three-component fusion protein acts as a functional transcription factor for a reporter gene. If the central target protein is relatively unstable it is more flexible and thereby allows the DNA binding domain and the transactivation domain to achieve an optimal orientation for transcriptional activation. Conversely, if the central target protein is highly stable it is too rigid to allow the DNA binding domain and the transactivation domain to achieve the proper orientation for transcriptional activation and thus is a less efficient transcription factor. To supplement the results obtained from the in vivo screen we also use the ORBIT suite of protein design algorithms to computationally generate stability variants. These algorithms enable one to mutate specific residues while keeping the remainder wild-type. Discrete sets of side chain rotamers are considered in the calculation and an empirical potential energy function is used to calculate the energies between rotamer pairs. The energies are subjected to a very fast side chain selection algorithm, based on the Dead-End Elimination theorem, which ultimately returns the global minimum energy conformation. We successfully demonstrated the ability of the in vivo chimeric stability screen and in silico ORBIT screen to generate novel protein variants with improved thermal stability.
Download or read book Protein Engineering written by Huimin Zhao and published by John Wiley & Sons. This book was released on 2021-08-23 with total page 41 pages. Available in PDF, EPUB and Kindle. Book excerpt: A one-stop reference that reviews protein design strategies to applications in industrial and medical biotechnology Protein Engineering: Tools and Applications is a comprehensive resource that offers a systematic and comprehensive review of the most recent advances in the field, and contains detailed information on the methodologies and strategies behind these approaches. The authors—noted experts on the topic—explore the distinctive advantages and disadvantages of the presented methodologies and strategies in a targeted and focused manner that allows for the adaptation and implementation of the strategies for new applications. The book contains information on the directed evolution, rational design, and semi-rational design of proteins and offers a review of the most recent applications in industrial and medical biotechnology. This important book: Covers technologies and methodologies used in protein engineering Includes the strategies behind the approaches, designed to help with the adaptation and implementation of these strategies for new applications Offers a comprehensive and thorough treatment of protein engineering from primary strategies to applications in industrial and medical biotechnology Presents cutting edge advances in the continuously evolving field of protein engineering Written for students and professionals of bioengineering, biotechnology, biochemistry, Protein Engineering: Tools and Applications offers an essential resource to the design strategies in protein engineering and reviews recent applications.
Download or read book Combinatorial Library written by Lisa B. English and published by Springer Science & Business Media. This book was released on 2008-02-04 with total page 380 pages. Available in PDF, EPUB and Kindle. Book excerpt: The continued successes of large- and small-scale genome sequencing projects are increasing the number of genomic targets available for drug d- covery at an exponential rate. In addition, a better understanding of molecular mechanisms—such as apoptosis, signal transduction, telomere control of ch- mosomes, cytoskeletal development, modulation of stress-related proteins, and cell surface display of antigens by the major histocompatibility complex m- ecules—has improved the probability of identifying the most promising genomic targets to counteract disease. As a result, developing and optimizing lead candidates for these targets and rapidly moving them into clinical trials is now a critical juncture in pharmaceutical research. Recent advances in com- natorial library synthesis, purification, and analysis techniques are not only increasing the numbers of compounds that can be tested against each specific genomic target, but are also speeding and improving the overall processes of lead discovery and optimization. There are two main approaches to combinatorial library production: p- allel chemical synthesis and split-and-mix chemical synthesis. These approaches can utilize solid- or solution-based synthetic methods, alone or in combination, although the majority of combinatorial library synthesis is still done on solid support. In a parallel synthesis, all the products are assembled separately in their own reaction vessels or microtiter plates. The array of rows and columns enables researchers to organize the building blocks to be c- bined, and provides an easy way to identify compounds in a particular well.
Download or read book De Novo Protein Design written by Sarbendra Lall Pradhananga and published by . This book was released on 2000 with total page 570 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Computational Design of Ligand Binding Proteins written by Barry L. Stoddard and published by Humana. This book was released on 2016-04-20 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume provides a collection of protocols and approaches for the creation of novel ligand binding proteins, compiled and described by many of today's leaders in the field of protein engineering. Chapters focus on modeling protein ligand binding sites, accurate modeling of protein-ligand conformational sampling, scoring of individual docked solutions, structure-based design program such as ROSETTA, protein engineering, and additional methodological approaches. Examples of applications include the design of metal-binding proteins and light-induced ligand binding proteins, the creation of binding proteins that also display catalytic activity, and the binding of larger peptide, protein, DNA and RNA ligands. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.
Download or read book Computational Protein Design written by Ilan Samish and published by Humana. This book was released on 2016-12-03 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: The aim this volume is to present the methods, challenges, software, and applications of this widespread and yet still evolving and maturing field. Computational Protein Design, the first book with this title, guides readers through computational protein design approaches, software and tailored solutions to specific case-study targets. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Computational Protein Design aims to ensure successful results in the further study of this vital field.
Download or read book Exploring Medical Biotechnology in vivo in vitro in silico written by Pratik Talukder and published by CRC Press. This book was released on 2024-04-25 with total page 435 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book on medical biotechnology offers a wide array of topics and cutting-edge research in the field featuring contributions from multiple authors, each specializing in their respective areas, making it highly valuable to science students and enthusiasts. The book provides comprehensive coverage on a diverse range of topics including sequence analysis, network pharmacology, drug discovery, CRISPR-Cas technology, precision medicine, neuroimaging biomarkers, therapeutics for neurodegenerative diseases, molecular pathogenesis of various diseases, plant-derived antioxidants, genetic approaches for disease diagnosis, cancer progression, immunotherapy, cancer biomarker identification, RNA Interference (RNAi) and nanotechnology in drug discovery and delivery, thus giving a holistic understanding of medical biotechnology. Each chapter delves into the latest research and developments in its respective field and offers readers insights into cutting-edge advancements in medical biotechnology. This up-to-date information will be invaluable to science students and enthusiasts who want to stay at the forefront of the field. The book adopts an interdisciplinary approach by incorporating elements of biology, genetics, computational techniques, nanotechnology and more, which enables readers to see the interconnectedness of different scientific disciplines and how they contribute to medical biotechnology. The book emphasizes practical applications, such as drug discovery, disease treatment, gene editing and targeted drug delivery. This focus on real-world applications is useful to readers interested in applying biotechnological techniques in the medical field. The book also acknowledges the serious challenges faced in the field of medical biotechnology and offers potential solutions to overcome these challenges to foster innovative thinking. As a reader, you will gain a comprehensive understanding of various aspects of medical biotechnology, equipping you with knowledge that can contribute to technological breakthroughs, advancements in medicine and the betterment of human life.
Download or read book In Silico Methods for Drug Design and Discovery written by Simone Brogi and published by Frontiers Media SA. This book was released on 2020-10-09 with total page 504 pages. Available in PDF, EPUB and Kindle. Book excerpt: This eBook is a collection of articles from a Frontiers Research Topic. Frontiers Research Topics are very popular trademarks of the Frontiers Journals Series: they are collections of at least ten articles, all centered on a particular subject. With their unique mix of varied contributions from Original Research to Review Articles, Frontiers Research Topics unify the most influential researchers, the latest key findings and historical advances in a hot research area! Find out more on how to host your own Frontiers Research Topic or contribute to one as an author by contacting the Frontiers Editorial Office: frontiersin.org/about/contact.
Download or read book Structural Biology in Drug Discovery written by Jean-Paul Renaud and published by John Wiley & Sons. This book was released on 2020-01-09 with total page 1367 pages. Available in PDF, EPUB and Kindle. Book excerpt: With the most comprehensive and up-to-date overview of structure-based drug discovery covering both experimental and computational approaches, Structural Biology in Drug Discovery: Methods, Techniques, and Practices describes principles, methods, applications, and emerging paradigms of structural biology as a tool for more efficient drug development. Coverage includes successful examples, academic and industry insights, novel concepts, and advances in a rapidly evolving field. The combined chapters, by authors writing from the frontlines of structural biology and drug discovery, give readers a valuable reference and resource that: Presents the benefits, limitations, and potentiality of major techniques in the field such as X-ray crystallography, NMR, neutron crystallography, cryo-EM, mass spectrometry and other biophysical techniques, and computational structural biology Includes detailed chapters on druggability, allostery, complementary use of thermodynamic and kinetic information, and powerful approaches such as structural chemogenomics and fragment-based drug design Emphasizes the need for the in-depth biophysical characterization of protein targets as well as of therapeutic proteins, and for a thorough quality assessment of experimental structures Illustrates advances in the field of established therapeutic targets like kinases, serine proteinases, GPCRs, and epigenetic proteins, and of more challenging ones like protein-protein interactions and intrinsically disordered proteins
Download or read book In Silico Drug Design written by Kunal Roy and published by Academic Press. This book was released on 2019-02-12 with total page 886 pages. Available in PDF, EPUB and Kindle. Book excerpt: In Silico Drug Design: Repurposing Techniques and Methodologies explores the application of computational tools that can be utilized for this approach. The book covers theoretical background and methodologies of chem-bioinformatic techniques and network modeling and discusses the various applied strategies to systematically retrieve, integrate and analyze datasets from diverse sources. Other topics include in silico drug design methods, computational workflows for drug repurposing, and network-based in silico screening for drug efficacy. With contributions from experts in the field and the inclusion of practical case studies, this book gives scientists, researchers and R&D professionals in the pharmaceutical industry valuable insights into drug design. Discusses the theoretical background and methodologies of useful techniques of cheminformatics and bioinformatics that can be applied for drug repurposing Offers case studies relating to the in silico modeling of FDA-approved drugs for the discovery of antifungal, anticancer, antiplatelet agents, and for drug therapies against diseases Covers tools and databases that can be utilized to facilitate in silico methods for drug repurposing
Download or read book Practical Protein Bioinformatics written by Florencio Pazos and published by Springer. This book was released on 2014-11-28 with total page 111 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book describes more than 60 web-accessible computational tools for protein analysis and is totally practical, with detailed explanations on how to use these tools and interpret their results and minimal mentions to their theoretical basis (only when that is required for making a better use of them). It covers a wide range of tools for dealing with different aspects of proteins, from their sequences, to their three-dimensional structures, and the biological networks they are immersed in. The selection of tools is based on the experience of the authors that lead a protein bioinformatics facility in a large research centre, with the additional constraint that the tools should be accessible through standard web browsers without requiring the local installation of specific software, command-line tools, etc. The web tools covered include those aimed to retrieve protein information, look for similar proteins, generate pair-wise and multiple sequence alignments of protein sequences, work with protein domains and motifs, study the phylogeny of a family of proteins, retrieve, manipulate and visualize protein three-dimensional structures, predict protein structural features as well as whole three-dimensional structures, extract biological information from protein structures, summarize large protein sets, study protein interaction and metabolic networks, etc. The book is associated to a dynamic web site that will reflect changes in the web addresses of the tools, updates of these, etc. It also contains QR codes that can be scanned with any device to direct its browser to the tool web site. This monograph will be most valuable for researchers in experimental labs without specific knowledge on bioinformatics or computing.
Download or read book Bioactive Proteins and Peptides as Functional Foods and Nutraceuticals written by Yoshinori Mine and published by John Wiley & Sons. This book was released on 2011-06-09 with total page 434 pages. Available in PDF, EPUB and Kindle. Book excerpt: Bioactive Proteins and Peptides as Functional Foods and Nutraceuticals highlights recent developments of nutraceutical proteins and peptides for the promotion of human health. The book considers fundamental concepts and structure-activity relations for the major classes of nutraceutical proteins and peptides. Coverage includes functional proteins and peptides from numerous sources including: soy, Pacific hake, bovine muscle, peas, wheat, fermented milk, eggs, casein, fish collagen, bovine lactoferrin, and rice. The international panel of experts from industry and academia also reviews current applications and future opportunities within the nutraceutical proteins and peptides sector.
Download or read book Translational Systems Biology Concepts and Practice for the Future of Biomedical Research written by Yoram Vodovotz and published by Academic Press. This book was released on 2017-11-13 with total page 178 pages. Available in PDF, EPUB and Kindle. Book excerpt: Are we satisfied with the rate of drug development? Are we happy with the drugs that come to market? Are we getting our money s worth in spending for basic biomedical research? In Translational Systems Biology, Drs. Yoram Vodovotz and Gary An address these questions by providing a foundational description the barriers facing biomedical research today and the immediate future, and how these barriers could be overcome through the adoption of a robust and scalable approach that will form the underpinning of biomedical research for the future. By using a combination of essays providing the intellectual basis of the Translational Dilemma and reports of examples in the study of inflammation, the content of Translational Systems Biology will remain relevant as technology and knowledge advances bring broad translational applicability to other diseases. Translational systems biology is an integrated, multi-scale, evidence-based approach that combines laboratory, clinical and computational methods with an explicit goal of developing effective means of control of biological processes for improving human health and rapid clinical application. This comprehensive approach to date has been utilized for in silico studies of sepsis, trauma, hemorrhage, and traumatic brain injury, acute liver failure, wound healing, and inflammation. Provides an explicit, reasoned, and systematic approach to dealing with the challenges of translational science across disciplines Establishes the case for including computational modeling at all stages of biomedical research and healthcare delivery, from early pre-clinical studies to long-term care, by clearly delineating efficiency and costs saving important to business investment Guides readers on how to communicate across domains and disciplines, particularly between biologists and computational researchers, to effectively develop multi- and trans-disciplinary research teams "
Download or read book Health Benefits of Green Tea written by Yukihiko Hara and published by CABI. This book was released on 2017-10-25 with total page 262 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book provides evidence to support the health-promoting components of green tea for human health. It explores the significance of green tea and its catechins represented by epigallocatechin gallate (EGCG), demonstrating their beneficial effects on diseases including cancer, obesity, arteriosclerosis, diabetes, hepatitis, and neurodegenerative diseases. The present status of human studies and avenues for future research are discussed. It is written by a team of experts from across the globe and makes significant Japanese findings available to international researchers. It is an essential resource for researchers interested in the biochemistry and pharmacology of green tea, and functional foods and beverages.
Download or read book Protein Structure Stability and Interactions written by John W. Shriver and published by Humana. This book was released on 2010-11-19 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: In the areas of biochemistry and cell biology, characterizations of stability and molecular interactions call for a quantitative approach with a level of precision that matches the fine tuning of these interactions in a living cell. Supporting and up-dating previous Methods in Molecular BiologyTM volumes, Protein Structure, Stability, and Interactions approaches its subject with a focus on theory and practical applications for both established methods as well as exciting new procedures. The volume presents an overview of many techniques currently used to study protein stability and interactions, including scanning and titration calorimetry, spectroscopic methods, high field NMR, and analytical ultracentrifugation. As a volume of the highly successful Methods in Molecular BiologyTM series, this work provides the kind of detailed description and implementation advice that is crucial for getting optimal results. Cutting-edge and easy to reference, Protein Structure, Stability, and Interactions is an ideal guide for all scientists interested in biomolecular interactions.
