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Author : Mária Ildikó Závodszky
Publisher :
ISBN 13 :
Total Pages : 344 pages
Book Rating : 4.3/5 (129 download)
Download or read book Modeling Flexibility in Protein-ligand Recognition written by Mária Ildikó Závodszky and published by . This book was released on 2003 with total page 344 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Author : Mark A. Williams
Publisher : Humana
ISBN 13 : 9781493958733
Total Pages : 0 pages
Book Rating : 4.9/5 (587 download)
Download or read book Protein-Ligand Interactions written by Mark A. Williams and published by Humana. This book was released on 2016-11-17 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Proteins are the cell’s workers, their messengers and overseers. In these roles, proteins specifically bind small molecules, nucleic acid and other protein partners. Cellular systems are closely regulated and biologically significant changes in populations of particular protein complexes correspond to very small variations of their thermodynamics or kinetics of reaction. Interfering with the interactions of proteins is the dominant strategy in the development of new pharmaceuticals. Protein Ligand Interactions: Methods and Applications, Second Edition provides a complete introduction to common and emerging procedures for characterizing the interactions of individual proteins. From the initial discovery of natural substrates or potential drug leads, to the detailed quantitative understanding of the mechanism of interaction, all stages of the research process are covered with a focus on those techniques that are, or are anticipated to become, widely accessible and performable with mainstream commercial instrumentation. Written in the highly successful Methods in Molecular Biology series format, chapters contain introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and notes on troubleshooting and avoiding known pitfalls. Authoritative and accessible, Protein Ligand Interactions: Methods and Applications, Second Edition serves as an ideal guide for researchers new to the field of biophysical characterization of protein interactions – whether they are beginning graduate students or experts in allied areas of molecular cell biology, microbiology, pharmacology, medicinal chemistry or structural biology.
Author : Holger Gohlke
Publisher : John Wiley & Sons
ISBN 13 : 3527645977
Total Pages : 359 pages
Book Rating : 4.5/5 (276 download)
Download or read book Protein-Ligand Interactions written by Holger Gohlke and published by John Wiley & Sons. This book was released on 2012-04-06 with total page 359 pages. Available in PDF, EPUB and Kindle. Book excerpt: Innovative and forward-looking, this volume focuses on recent achievements in this rapidly progressing field and looks at future potential for development. The first part provides a basic understanding of the factors governing protein-ligand interactions, followed by a comparison of key experimental methods (calorimetry, surface plasmon resonance, NMR) used in generating interaction data. The second half of the book is devoted to insilico methods of modeling and predicting molecular recognition and binding, ranging from first principles-based to approximate ones. Here, as elsewhere in the book, emphasis is placed on novel approaches and recent improvements to established methods. The final part looks at unresolved challenges, and the strategies to address them. With the content relevant for all drug classes and therapeutic fields, this is an inspiring and often-consulted guide to the complexity of protein-ligand interaction modeling and analysis for both novices and experts.
Author : Yee Siew Choong
Publisher : Bentham Science Publishers
ISBN 13 : 981516547X
Total Pages : 159 pages
Book Rating : 4.8/5 (151 download)
Download or read book Computational Modeling and Simulation in Biomedical Research written by Yee Siew Choong and published by Bentham Science Publishers. This book was released on 2024-08-01 with total page 159 pages. Available in PDF, EPUB and Kindle. Book excerpt: This reference provides a comprehensive overview of computational modelling and simulation for theoretical and practical biomedical research. The book explains basic concepts of computational biology and data modelling for learners and early career researchers. Chapters cover these topics: 1. An introduction to computational tools in biomedical research 2. Computational analysis of biological data 3. Algorithm development for computational modelling and simulation 4. The roles and application of protein modelling in biomedical research 5. Dynamics of biomolecular ligand recognition Key features include a simple, easy-to-understand presentation, detailed explanation of important concepts in computational modeling and simulations and references.
Author : Claudio N. Cavasotto
Publisher : CRC Press
ISBN 13 : 1482217856
Total Pages : 539 pages
Book Rating : 4.4/5 (822 download)
Download or read book In Silico Drug Discovery and Design written by Claudio N. Cavasotto and published by CRC Press. This book was released on 2015-08-06 with total page 539 pages. Available in PDF, EPUB and Kindle. Book excerpt: In Silico Drug Discovery and Design: Theory, Methods, Challenges, and Applications provides a comprehensive, unified, and in-depth overview of the current methodological strategies in computer-aided drug discovery and design. Its main aims are to introduce the theoretical framework and algorithms, discuss the range of validity, strengths and limita
Author : Adriano D. Andricopulo
Publisher : Frontiers Media SA
ISBN 13 : 2889457443
Total Pages : 415 pages
Book Rating : 4.8/5 (894 download)
Download or read book Chemoinformatics Approaches to Structure- and Ligand-Based Drug Design written by Adriano D. Andricopulo and published by Frontiers Media SA. This book was released on 2019-02-05 with total page 415 pages. Available in PDF, EPUB and Kindle. Book excerpt: Chemoinformatics is paramount to current drug discovery. Structure- and ligand-based drug design strategies have been used to uncover hidden patterns in large amounts of data, and to disclose the molecular aspects underlying ligand-receptor interactions. This Research Topic aims to share with a broad audience the most recent trends in the use of chemoinformatics in drug design. To that end, experts in all areas of drug discovery have made their knowledge available through a series of articles that report state-of-the-art approaches. Readers are provided with outstanding contributions focusing on a wide variety of topics which will be of great value to those interested in the many different and exciting facets of drug design.
Author : Supratik Kar
Publisher : Springer Nature
ISBN 13 : 3031338715
Total Pages : 311 pages
Book Rating : 4.0/5 (313 download)
Download or read book Current Trends in Computational Modeling for Drug Discovery written by Supratik Kar and published by Springer Nature. This book was released on 2023-06-30 with total page 311 pages. Available in PDF, EPUB and Kindle. Book excerpt: This contributed volume offers a comprehensive discussion on how to design and discover pharmaceuticals using computational modeling techniques. The different chapters deal with the classical and most advanced techniques, theories, protocols, databases, and tools employed in computer-aided drug design (CADD) covering diverse therapeutic classes. Multiple components of Structure-Based Drug Discovery (SBDD) along with its workflow and associated challenges are presented while potential leads for Alzheimer’s disease (AD), antiviral agents, anti-human immunodeficiency virus (HIV) drugs, and leads for Severe Fever with Thrombocytopenia Syndrome Virus (SFTSV) disease are discussed in detail. Computational toxicological aspects in drug design and discovery, screening adverse effects, and existing or future in silico tools are highlighted, while a novel in silico tool, RASAR, which can be a major technique for small to big datasets when not much experimental data are present, is presented. The book also introduces the reader to the major drug databases covering drug molecules, chemicals, therapeutic targets, metabolomics, and peptides, which are great resources for drug discovery employing drug repurposing, high throughput, and virtual screening. This volume is a great tool for graduates, researchers, academics, and industrial scientists working in the fields of cheminformatics, bioinformatics, computational biology, and chemistry.
Author : Zaheer Ul-Haq
Publisher : Elsevier
ISBN 13 : 1608058646
Total Pages : 364 pages
Book Rating : 4.6/5 (8 download)
Download or read book Frontiers in Computational Chemistry: Volume 1 written by Zaheer Ul-Haq and published by Elsevier. This book was released on 2015-12-14 with total page 364 pages. Available in PDF, EPUB and Kindle. Book excerpt: Frontiers in Computational Chemistry, originally published by Bentham and now distributed by Elsevier, presents the latest research findings and methods in the diverse field of computational chemistry, focusing on molecular modeling techniques used in drug discovery and the drug development process. This includes computer-aided molecular design, drug discovery and development, lead generation, lead optimization, database management, computer and molecular graphics, and the development of new computational methods or efficient algorithms for the simulation of chemical phenomena including analyses of biological activity. In Volume 1, the leading researchers in the field have collected eight different perspectives in the application of computational methods towards drug design to provide an up-to-date rendering of the current field. This volume covers a variety of topics from G protein-coupled receptors, to the use of cheminformatics and bioinformatics, computational tools such as Molecular Mechanics Poisson-Boltzmann Surface Area, protein-protein interactions, the use of computational methods on large biological data sets, various computational methods used to identify pharmaceutically relevant targets, and more. - Brings together a wide range of research into a single collection to help researchers keep up with new methods - Uniquely focuses on computational chemistry approaches that can accelerate drug design - Makes a solid connection between experiment and computation and the novel application of computational methods in the fields of biology, chemistry, biochemistry, physics, and biophysics, with particular focus on the integration of computational methods with experimental data
Author : Jerzy Leszczynski
Publisher : Springer Science & Business Media
ISBN 13 : 9400707118
Total Pages : 1451 pages
Book Rating : 4.4/5 (7 download)
Download or read book Handbook of Computational Chemistry written by Jerzy Leszczynski and published by Springer Science & Business Media. This book was released on 2012-01-13 with total page 1451 pages. Available in PDF, EPUB and Kindle. Book excerpt: The role the Handbook of Computational Chemistry is threefold. It is primarily intended to be used as a guide that navigates the user through the plethora of computational methods currently in use; it explains their limitations and advantages; and it provides various examples of their important and varied applications. This reference work is presented in three volumes. Volume I introduces the different methods used in computational chemistry. Basic assumptions common to the majority of computational methods based on molecular, quantum, or statistical mechanics are outlined and special attention is paid to the limits of their applicability. Volume II portrays the applications of computational methods to model systems and discusses in detail molecular structures, the modelling of various properties of molecules and chemical reactions. Both ground and excited states properties are covered in the gas phase as well as in solution. This volume also describes Nanomaterials and covers topics such as clusters, periodic, and nano systems. Special emphasis is placed on the environmental effects of nanostructures. Volume III is devoted to the important class of Biomolecules. Useful models of biological systems considered by computational chemists are provided and RNA, DNA and proteins are discussed in detail. This volume presents examples of calcualtions of their properties and interactions and reveals the role of solvents in biologically important reactions as well as the structure function relationship of various classes of Biomolecules.
Author : Simone Brogi
Publisher : Frontiers Media SA
ISBN 13 : 2889660575
Total Pages : 504 pages
Book Rating : 4.8/5 (896 download)
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.
Author : Holger Gohlke
Publisher : John Wiley & Sons
ISBN 13 : 3527329668
Total Pages : 361 pages
Book Rating : 4.5/5 (273 download)
Download or read book Protein-Ligand Interactions written by Holger Gohlke and published by John Wiley & Sons. This book was released on 2012-05-21 with total page 361 pages. Available in PDF, EPUB and Kindle. Book excerpt: Innovative and forward-looking, this volume focuses on recent achievements in this rapidly progressing field and looks at future potential for development. The first part provides a basic understanding of the factors governing protein-ligand interactions, followed by a comparison of key experimental methods (calorimetry, surface plasmon resonance, NMR) used in generating interaction data. The second half of the book is devoted to insilico methods of modeling and predicting molecular recognition and binding, ranging from first principles-based to approximate ones. Here, as elsewhere in the book, emphasis is placed on novel approaches and recent improvements to established methods. The final part looks at unresolved challenges, and the strategies to address them. With the content relevant for all drug classes and therapeutic fields, this is an inspiring and often-consulted guide to the complexity of protein-ligand interaction modeling and analysis for both novices and experts.
Author : Valerie Daggett
Publisher : Elsevier
ISBN 13 : 0080493785
Total Pages : 477 pages
Book Rating : 4.0/5 (84 download)
Download or read book Protein Simulations written by Valerie Daggett and published by Elsevier. This book was released on 2003-11-26 with total page 477 pages. Available in PDF, EPUB and Kindle. Book excerpt: Protein Simulation focuses on predicting how protein will act in vivo. These studies use computer analysis, computer modeling, and statistical probability to predict protein function.* Force Fields* Ligand Binding* Protein Membrane Simulation* Enzyme Dynamics* Protein Folding and unfolding simulations
Author : Timir Tripathi
Publisher : Academic Press
ISBN 13 : 0323902650
Total Pages : 716 pages
Book Rating : 4.3/5 (239 download)
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
Author : Ke-li Han
Publisher : Springer Science & Business Media
ISBN 13 : 3319029703
Total Pages : 488 pages
Book Rating : 4.3/5 (19 download)
Download or read book Protein Conformational Dynamics written by Ke-li Han and published by Springer Science & Business Media. This book was released on 2014-01-20 with total page 488 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book discusses how biological molecules exert their function and regulate biological processes, with a clear focus on how conformational dynamics of proteins are critical in this respect. In the last decade, the advancements in computational biology, nuclear magnetic resonance including paramagnetic relaxation enhancement, and fluorescence-based ensemble/single-molecule techniques have shown that biological molecules (proteins, DNAs and RNAs) fluctuate under equilibrium conditions. The conformational and energetic spaces that these fluctuations explore likely contain active conformations that are critical for their function. More interestingly, these fluctuations can respond actively to external cues, which introduces layers of tight regulation on the biological processes that they dictate. A growing number of studies have suggested that conformational dynamics of proteins govern their role in regulating biological functions, examples of this regulation can be found in signal transduction, molecular recognition, apoptosis, protein / ion / other molecules translocation and gene expression. On the experimental side, the technical advances have offered deep insights into the conformational motions of a number of proteins. These studies greatly enrich our knowledge of the interplay between structure and function. On the theoretical side, novel approaches and detailed computational simulations have provided powerful tools in the study of enzyme catalysis, protein / drug design, protein / ion / other molecule translocation and protein folding/aggregation, to name but a few. This work contains detailed information, not only on the conformational motions of biological systems, but also on the potential governing forces of conformational dynamics (transient interactions, chemical and physical origins, thermodynamic properties). New developments in computational simulations will greatly enhance our understanding of how these molecules function in various biological events.
Author : Colin Kleanthous
Publisher : Frontiers in Molecular Biology
ISBN 13 : 9780199637607
Total Pages : 370 pages
Book Rating : 4.6/5 (376 download)
Download or read book Protein-protein Recognition written by Colin Kleanthous and published by Frontiers in Molecular Biology. This book was released on 2000 with total page 370 pages. Available in PDF, EPUB and Kindle. Book excerpt: The purpose of Protein-Protein Recognition is to bring together concepts and systems pertaining to protein-protein interactions in a single unifying volume. In the light of the information from the genome sequencing projects and the increase in structural information it is an opportune time totry to make generalizations about how and why proteins form complexes with each other. The emphasis of the book is on heteromeric complexes (complexes in which each of the components can exist in an unbound state) and will use well-studied model systems to explain the processes of formingcomplexes. After an introductory section on the kinetics, thermodynamics, analysis, and classification of protein-protein interactions, weak, intermediate, and high affinity complexes are dealt with in turn. Weak affinity complexes are represented by electron transfer proteins and integrincomplexes. Anti-lysozyme antibodies, the MHC proteins and their interactions with T-cell receptors, and the protein interactions of eukaryotic signal transduction are the systems used to explain complexes with intermediate affinities. Finally, tight binding complexes are represented by theinteraction of protein inhibitors with serine proteases and by nuclease inhibitor complexes. Throughout the chapters common themes are the technologies which have had the greatest impact, how specificity is determined, how complexes are stabilized, and medical and industrial applications.
Author : Alan Hinchliffe
Publisher : Royal Society of Chemistry
ISBN 13 : 1847555268
Total Pages : 543 pages
Book Rating : 4.8/5 (475 download)
Download or read book Chemical Modelling written by Alan Hinchliffe and published by Royal Society of Chemistry. This book was released on 2007-10-31 with total page 543 pages. Available in PDF, EPUB and Kindle. Book excerpt: Chemical Modelling: Applications and Theory comprises critical literature reviews of molecular modelling, both theoretical and applied. Molecular modelling in this context refers to modelling the structure, properties and reactions of atoms, molecules & materials. Each chapter is compiled by experts in their fields and provides a selective review of recent literature. With chemical modelling covering such a wide range of subjects, this Specialist Periodical Report serves as the first port of call to any chemist, biochemist, materials scientist or molecular physicist needing to acquaint themselves of major developments in the area. Specialist Periodical Reports provide systematic and detailed review coverage in major areas of chemical research. Compiled by teams of leading authorities in the relevant subject areas, the series creates a unique service for the active research chemist, with regular, in-depth accounts of progress in particular fields of chemistry. Subject coverage within different volumes of a given title is similar and publication is on an annual or biennial basis. Current subject areas covered are Amino Acids, Peptides and Proteins, Carbohydrate Chemistry, Catalysis, Chemical Modelling. Applications and Theory, Electron Paramagnetic Resonance, Nuclear Magnetic Resonance, Organometallic Chemistry. Organophosphorus Chemistry, Photochemistry and Spectroscopic Properties of Inorganic and Organometallic Compounds. From time to time, the series has altered according to the fluctuating degrees of activity in the various fields, but these volumes remain a superb reference point for researchers.
Author : Nikolay V Dokholyan
Publisher : Springer Science & Business Media
ISBN 13 : 1461421454
Total Pages : 360 pages
Book Rating : 4.4/5 (614 download)
Download or read book Computational Modeling of Biological Systems written by Nikolay V Dokholyan and published by Springer Science & Business Media. This book was released on 2012-02-12 with total page 360 pages. Available in PDF, EPUB and Kindle. Book excerpt: Computational modeling is emerging as a powerful new approach to study and manipulate biological systems. Multiple methods have been developed to model, visualize, and rationally alter systems at various length scales, starting from molecular modeling and design at atomic resolution to cellular pathways modeling and analysis. Higher time and length scale processes, such as molecular evolution, have also greatly benefited from new breeds of computational approaches. This book provides an overview of the established computational methods used for modeling biologically and medically relevant systems.
