G Protein Coupled Receptors Modeling And Simulation

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G Protein-Coupled Receptors - Modeling and Simulation

Author : Marta Filizola
Publisher : Springer Science & Business Media
ISBN 13 : 9400774230
Total Pages : 228 pages
Book Rating : 4.4/5 (7 download)

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Book Synopsis G Protein-Coupled Receptors - Modeling and Simulation by : Marta Filizola

Download or read book G Protein-Coupled Receptors - Modeling and Simulation written by Marta Filizola and published by Springer Science & Business Media. This book was released on 2013-10-25 with total page 228 pages. Available in PDF, EPUB and Kindle. Book excerpt: G protein-coupled receptors (GPCRs) are heptahelical transmembrane receptors that convert extra-cellular stimuli into intra-cellular signaling, and ultimately into biological responses. Since GPCRs are natural targets for approximately 40% of all modern medicines, it is not surprising that they have been the subject of intense research. Notwithstanding the amount of data generated over the years, discovering ligands of these receptors with optimal therapeutic properties is not straightforward and has certainly been hampered for years by the lack of high-resolution structural information about these receptors. Luckily, there has been a steady increase of high-resolution crystal structures of these receptors since 2007, and this information, integrated with dynamic inferences from computational and experimental methods, holds great potential for the discovery of new, improved drugs. This book, which provides, for the first time, state-of-the-art views on modeling and simulation of GPCRs, is divided into 4 parts. In the first part, the impact of currently available GPCR crystal structures on structural modeling is discussed extensively as are critical insights from simulations in the second part of the book. The third part reports recent progress in rational ligand discovery and mathematical modeling, whereas the fourth part provides an overview of bioinformatics tools and resources that are available for GPCRs.

A New Modeling Protocol for G-protein Coupled Receptors

Author : Andrew W. Mauk
Publisher :
ISBN 13 :
Total Pages : 364 pages
Book Rating : 4.:/5 (348 download)

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Book Synopsis A New Modeling Protocol for G-protein Coupled Receptors by : Andrew W. Mauk

Download or read book A New Modeling Protocol for G-protein Coupled Receptors written by Andrew W. Mauk and published by . This book was released on 1996 with total page 364 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Modelling of GPCRs

Author : Andrea Strasser
Publisher : Springer Science & Business Media
ISBN 13 : 9400745966
Total Pages : 219 pages
Book Rating : 4.4/5 (7 download)

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Book Synopsis Modelling of GPCRs by : Andrea Strasser

Download or read book Modelling of GPCRs written by Andrea Strasser and published by Springer Science & Business Media. This book was released on 2012-08-13 with total page 219 pages. Available in PDF, EPUB and Kindle. Book excerpt: G protein coupled receptors (GPCRs) comprise an important protein family, which is involved in signal transduction in the cell. Besides that a large number of drugs, available on market, address GPCRs. For an efficient and improved development of appropriate drugs, molecular modelling of GPCRs is – in order to understand the ligand-receptor interactions and functionality of GPCRs on molecular level - an important tool. The book “Modelling of GPCRs – a practical handbook” is focussed onto a practical introduction into molecular modelling of GPCRs. This book is very useful for beginners in GPCR modelling, but also addresses the advanced GPCR modeller: On the one hand, the book introduces principles of GPCR modelling, including extensive examples. On the other hand, detailed outlooks onto advanced GPCR modelling techniques are presented. Furthermore, the book includes important data, like information about crystal structures in a summarized manner or amino acid sequences, which are essential for GPCR modelling in general. Due to an increase in efficacy and data handling most modellers use LINUX as operating system. To address this, a summary of most important LINUX commands with examples is presented within the book.

G Protein Coupled Receptors

Author :
Publisher : Academic Press
ISBN 13 : 012407944X
Total Pages : 541 pages
Book Rating : 4.1/5 (24 download)

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Book Synopsis G Protein Coupled Receptors by :

Download or read book G Protein Coupled Receptors written by and published by Academic Press. This book was released on 2013-01-28 with total page 541 pages. Available in PDF, EPUB and Kindle. Book excerpt: This new volume of Methods in Enzymology continues the legacy of this premier serial with quality chapters authored by leaders in the field. This volume covers G protein coupled receptors, and includes chapters on such topics as GPCR modelling, interactions with other molecules, virtual screening and GPCR activation. - Continues the legacy of this premier serial with quality chapters authored by leaders in the field - Covers G protein coupled receptors - Contains chapters on such topics as GPCR modelling, interactions with other molecules, virtual screening and GPCR activation

G Protein-Coupled Receptors

Author : Jesus Giraldo
Publisher : Royal Society of Chemistry
ISBN 13 : 1849733449
Total Pages : 549 pages
Book Rating : 4.8/5 (497 download)

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Book Synopsis G Protein-Coupled Receptors by : Jesus Giraldo

Download or read book G Protein-Coupled Receptors written by Jesus Giraldo and published by Royal Society of Chemistry. This book was released on 2011-08-16 with total page 549 pages. Available in PDF, EPUB and Kindle. Book excerpt: G protein-coupled receptors (GPCRs) are the largest family of cell-surface receptors, with more than 800 members identified thus far in the human genome. They regulate the function of most cells in the body, and represent approximately 3% of the genes in the human genome. These receptors respond to a wide variety of structurally diverse ligands, ranging from small molecules, such as biogenic amines, nucleotides and ions, to lipids, peptides, proteins, and even light. Ligands (agonists and antagonists) acting on GPCRs are important in the treatment of numerous diseases, including cardiovascular and mental disorders, retinal degeneration, cancer, and AIDS. It is estimated that these receptors represent about one third of the actual identified targets of clinically used drugs. The determination of rhodopsin crystal structure and, more recently, of opsin, 1 and 2 adrenergic and A2A adenosine receptors provides both academia and industry with extremely valuable data for a better understanding of the molecular determinants of receptor function and a more reliable rationale for drug design. GPCR structure and function constitutes a hot topic. The book, which lies between the fields of chemical biology, molecular pharmacology and medicinal chemistry, is divided into three parts. The first part considers what receptor structures tell us about the mechanism of receptor activation. Part II focuses on receptor function. It discusses what the data from biophysical and mutational studies, and the analysis of the interactions of the receptor with ligands and regulator proteins, tell us about the process of signal transduction. The final part, on modelling and simulation, details new insights on the link between structure and mechanism and their implications in drug design.

Molecular Dynamics Simulations of Seven-transmembrane Receptors

Author :
Publisher :
ISBN 13 :
Total Pages : pages
Book Rating : 4.:/5 (65 download)

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Book Synopsis Molecular Dynamics Simulations of Seven-transmembrane Receptors by :

Download or read book Molecular Dynamics Simulations of Seven-transmembrane Receptors written by and published by . This book was released on 2003 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: ABSTRACT Seven transmembrane (7-TM) G protein coupled receptors (GPCR) constitute the largest family of integral membrane proteins in eukaryotes with more than 1000 members and encoding more than 2% of the human genome. These proteins play a key role in the transmission and transduction of cellular signals responding to hormones, neurotransmitters, light and other agonists, regulating basic biological processes. Their natural abundance together with their localization in the cell membrane makes them suitable targets for therapeutic intervention. Consequently, GPCR are proteins with enormous pharmacologic interest, representing the targets of about 50% of the currently marketed drugs. The current limitations in the experimental techniques necessary for microscopic studies of the membrane as well as membrane proteins emerged the use of computational methods and specifically molecular dynamics simulations. The lead motif of this thesis is the study of GPCR by means of this technique, with the ultimate goal of developing a methodology that can be generalized to the study of most 7-TM as well as other membrane proteins. Since the bovine rhodopsin was the only protein of the GPCR family with a known threedimensional structure at an atomic level until very recently, most of the effort is centered in the study of this receptor as a model of GPCR. The scope of this thesis is twofold. On the one hand it addresses the study of the simulation conditions, including the procedure as well as the sampling box to get optimal results, and on the other, the biological implications of the structural and dynamical behavior observed in the simulations. Specifically, regarding the methodological aspects of the work, the bovine rhodopsin has been studied using different treatments of long-range electrostatic interactions and sampling conditions, as well as the effect of sampling the protein embedded in different one-component lipid bilayers. The binding of ions to lipid bilayers in the abs.

Ligand Design for G Protein-coupled Receptors

Author : Didier Rognan
Publisher : John Wiley & Sons
ISBN 13 : 3527608265
Total Pages : 284 pages
Book Rating : 4.5/5 (276 download)

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Book Synopsis Ligand Design for G Protein-coupled Receptors by : Didier Rognan

Download or read book Ligand Design for G Protein-coupled Receptors written by Didier Rognan and published by John Wiley & Sons. This book was released on 2006-08-21 with total page 284 pages. Available in PDF, EPUB and Kindle. Book excerpt: G protein-coupled receptors (GPCRs) are one of the most important target classes in pharmacology and are the target of many blockbuster drugs. Yet only with the recent elucidation of the rhodopsin structure have these receptors become amenable to a rational drug design. Based on recent examples from academia and the pharmaceutical industry, this book demonstrates how to apply the whole range of bioinformatics, chemoinformatics and molecular modeling tools to the rational design of novel drugs targeting GPCRs. Essential reading for medicinal chemists and drug designers working with this largest class of drug targets in the human genome.

Insight Into G Protein-coupled Receptors Through Molecular Dynamics Simulations

Author : Silvia Atanasio
Publisher :
ISBN 13 :
Total Pages : pages
Book Rating : 4.:/5 (124 download)

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Book Synopsis Insight Into G Protein-coupled Receptors Through Molecular Dynamics Simulations by : Silvia Atanasio

Download or read book Insight Into G Protein-coupled Receptors Through Molecular Dynamics Simulations written by Silvia Atanasio and published by . This book was released on 2021 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:

Molecular Modeling in Drug Design

Author : Rebecca Wade
Publisher : MDPI
ISBN 13 : 3038976148
Total Pages : 220 pages
Book Rating : 4.0/5 (389 download)

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Book Synopsis Molecular Modeling in Drug Design by : Rebecca Wade

Download or read book Molecular Modeling in Drug Design written by Rebecca Wade and published by MDPI. This book was released on 2019-03-26 with total page 220 pages. Available in PDF, EPUB and Kindle. Book excerpt: Since the first attempts at structure-based drug design about four decades ago, molecular modelling techniques for drug design have developed enormously, along with the increasing computational power and structural and biological information of active compounds and potential target molecules. Nowadays, molecular modeling can be considered to be an integral component of the modern drug discovery and development toolbox. Nevertheless, there are still many methodological challenges to be overcome in the application of molecular modeling approaches to drug discovery. The eight original research and five review articles collected in this book provide a snapshot of the state-of-the-art of molecular modeling in drug design, illustrating recent advances and critically discussing important challenges. The topics covered include virtual screening and pharmacophore modelling, chemoinformatic applications of artificial intelligence and machine learning, molecular dynamics simulation and enhanced sampling to investigate contributions of molecular flexibility to drug–receptor interactions, the modeling of drug–receptor solvation, hydrogen bonding and polarization, and drug design against protein–protein interfaces and membrane protein receptors.

G Protein-Coupled Receptors Part A

Author :
Publisher : Academic Press
ISBN 13 : 0128133201
Total Pages : 262 pages
Book Rating : 4.1/5 (281 download)

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Book Synopsis G Protein-Coupled Receptors Part A by :

Download or read book G Protein-Coupled Receptors Part A written by and published by Academic Press. This book was released on 2017-10-02 with total page 262 pages. Available in PDF, EPUB and Kindle. Book excerpt: G Protein Coupled Receptors, Second Edition, Volume 143, a new volume in the Methods in Cell Biology series, continues the legacy of this premier serial with quality chapters authored by leaders in the field. It contains a wide array of topics about the G protein coupled receptors, as well as updates of chapters from the first edition. - Contains contributions from experts in the field from across the world - Covers a wide array of topics on G protein coupled receptors - Includes analysis based topics

Computational Modeling of Protein-small-molecule Interactions

Author : Kristina Elisabet Furse
Publisher :
ISBN 13 :
Total Pages : 366 pages
Book Rating : 4.:/5 (76 download)

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Book Synopsis Computational Modeling of Protein-small-molecule Interactions by : Kristina Elisabet Furse

Download or read book Computational Modeling of Protein-small-molecule Interactions written by Kristina Elisabet Furse and published by . This book was released on 2005 with total page 366 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Statistical Physics of Biomolecules

Author : Daniel M. Zuckerman
Publisher : CRC Press
ISBN 13 : 1420073796
Total Pages : 356 pages
Book Rating : 4.4/5 (2 download)

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Book Synopsis Statistical Physics of Biomolecules by : Daniel M. Zuckerman

Download or read book Statistical Physics of Biomolecules written by Daniel M. Zuckerman and published by CRC Press. This book was released on 2010-06-02 with total page 356 pages. Available in PDF, EPUB and Kindle. Book excerpt: From the hydrophobic effect to protein-ligand binding, statistical physics is relevant in almost all areas of molecular biophysics and biochemistry, making it essential for modern students of molecular behavior. But traditional presentations of this material are often difficult to penetrate. Statistical Physics of Biomolecules: An Introduction brin

Biomolecular Simulations in Structure-Based Drug Discovery

Author : Francesco L. Gervasio
Publisher : John Wiley & Sons
ISBN 13 : 3527342656
Total Pages : 368 pages
Book Rating : 4.5/5 (273 download)

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Book Synopsis Biomolecular Simulations in Structure-Based Drug Discovery by : Francesco L. Gervasio

Download or read book Biomolecular Simulations in Structure-Based Drug Discovery written by Francesco L. Gervasio and published by John Wiley & Sons. This book was released on 2019-04-29 with total page 368 pages. Available in PDF, EPUB and Kindle. Book excerpt: A guide to applying the power of modern simulation tools to better drug design Biomolecular Simulations in Structure-based Drug Discovery offers an up-to-date and comprehensive review of modern simulation tools and their applications in real-life drug discovery, for better and quicker results in structure-based drug design. The authors describe common tools used in the biomolecular simulation of drugs and their targets and offer an analysis of the accuracy of the predictions. They also show how to integrate modeling with other experimental data. Filled with numerous case studies from different therapeutic fields, the book helps professionals to quickly adopt these new methods for their current projects. Experts from the pharmaceutical industry and academic institutions present real-life examples for important target classes such as GPCRs, ion channels and amyloids as well as for common challenges in structure-based drug discovery. Biomolecular Simulations in Structure-based Drug Discovery is an important resource that: -Contains a review of the current generation of biomolecular simulation tools that have the robustness and speed that allows them to be used as routine tools by non-specialists -Includes information on the novel methods and strategies for the modeling of drug-target interactions within the framework of real-life drug discovery and development -Offers numerous illustrative case studies from a wide-range of therapeutic fields -Presents an application-oriented reference that is ideal for those working in the various fields Written for medicinal chemists, professionals in the pharmaceutical industry, and pharmaceutical chemists, Biomolecular Simulations in Structure-based Drug Discovery is a comprehensive resource to modern simulation tools that complement and have the potential to complement or replace laboratory assays for better results in drug design.

An Introduction to Markov State Models and Their Application to Long Timescale Molecular Simulation

Author : Gregory R. Bowman
Publisher : Springer Science & Business Media
ISBN 13 : 9400776063
Total Pages : 148 pages
Book Rating : 4.4/5 (7 download)

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Book Synopsis An Introduction to Markov State Models and Their Application to Long Timescale Molecular Simulation by : Gregory R. Bowman

Download or read book An Introduction to Markov State Models and Their Application to Long Timescale Molecular Simulation written by Gregory R. Bowman and published by Springer Science & Business Media. This book was released on 2013-12-02 with total page 148 pages. Available in PDF, EPUB and Kindle. Book excerpt: The aim of this book volume is to explain the importance of Markov state models to molecular simulation, how they work, and how they can be applied to a range of problems. The Markov state model (MSM) approach aims to address two key challenges of molecular simulation: 1) How to reach long timescales using short simulations of detailed molecular models. 2) How to systematically gain insight from the resulting sea of data. MSMs do this by providing a compact representation of the vast conformational space available to biomolecules by decomposing it into states sets of rapidly interconverting conformations and the rates of transitioning between states. This kinetic definition allows one to easily vary the temporal and spatial resolution of an MSM from high-resolution models capable of quantitative agreement with (or prediction of) experiment to low-resolution models that facilitate understanding. Additionally, MSMs facilitate the calculation of quantities that are difficult to obtain from more direct MD analyses, such as the ensemble of transition pathways. This book introduces the mathematical foundations of Markov models, how they can be used to analyze simulations and drive efficient simulations, and some of the insights these models have yielded in a variety of applications of molecular simulation.

The Dynamic Coupling Interface of G-protein Coupled Receptors

Author :
Publisher :
ISBN 13 :
Total Pages : 139 pages
Book Rating : 4.:/5 (915 download)

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Book Synopsis The Dynamic Coupling Interface of G-protein Coupled Receptors by :

Download or read book The Dynamic Coupling Interface of G-protein Coupled Receptors written by and published by . This book was released on 2015 with total page 139 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Allosteric Modulation of G Protein-Coupled Receptors

Author : Robert Laprairie
Publisher : Academic Press
ISBN 13 : 0128197722
Total Pages : 214 pages
Book Rating : 4.1/5 (281 download)

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Book Synopsis Allosteric Modulation of G Protein-Coupled Receptors by : Robert Laprairie

Download or read book Allosteric Modulation of G Protein-Coupled Receptors written by Robert Laprairie and published by Academic Press. This book was released on 2022-02-05 with total page 214 pages. Available in PDF, EPUB and Kindle. Book excerpt: Allosteric Modulation of G Protein-Coupled Receptors reviews fundamental information on G protein-coupled receptors (GPCRs) and allosteric modulation, presenting original research in the area and collectively providing a comprehensive description of key issues in GPCR allosteric modulation. The book provides background on core concepts of molecular pharmacology while also introducing the most important advances and studies in the area. It also discusses key methodologies. This is an essential book for researchers and advanced students engaged in pharmacology, toxicology and pharmaceutical sciences training and research. Many of the GPCR-targeted drugs released in the past decade have specifically worked via allosteric mechanisms. Unlike direct orthosteric-acting compounds that occupy a similar receptor site to that of endogenous ligands, allosteric modulators alter GPCR-dependent signaling at a site apart from the endogenous ligand. Recent methodological and analytical advances have greatly improved our ability to understand the signaling mechanisms of GPCRs. We now know that allostery is a common regulatory mechanism for all GPCRs and not – as we once believed – unique to a few receptor subfamilies. - Introduces background on core concepts of molecular pharmacology, including statistical analyses, non-linear regression, complex models and GPCR-dependent signal transduction as they relate to allosteric modulation - Discusses critical advances and landmark studies, including discoveries in the area of GPCR allosteric modulation, which are reviewed for their importance in positive and negative regulation, protein-protein interactions, and small molecule drug discovery - Includes key methodologies used to study allosteric modulation at the in silico, in vitro, and in vivo levels of drug discovery and characterization

Biomolecular Simulations in Structure-Based Drug Discovery

Author : Francesco L. Gervasio
Publisher : John Wiley & Sons
ISBN 13 : 3527806857
Total Pages : 420 pages
Book Rating : 4.5/5 (278 download)

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Book Synopsis Biomolecular Simulations in Structure-Based Drug Discovery by : Francesco L. Gervasio

Download or read book Biomolecular Simulations in Structure-Based Drug Discovery written by Francesco L. Gervasio and published by John Wiley & Sons. This book was released on 2019-01-04 with total page 420 pages. Available in PDF, EPUB and Kindle. Book excerpt: A guide to applying the power of modern simulation tools to better drug design Biomolecular Simulations in Structure-based Drug Discovery offers an up-to-date and comprehensive review of modern simulation tools and their applications in real-life drug discovery, for better and quicker results in structure-based drug design. The authors describe common tools used in the biomolecular simulation of drugs and their targets and offer an analysis of the accuracy of the predictions. They also show how to integrate modeling with other experimental data. Filled with numerous case studies from different therapeutic fields, the book helps professionals to quickly adopt these new methods for their current projects. Experts from the pharmaceutical industry and academic institutions present real-life examples for important target classes such as GPCRs, ion channels and amyloids as well as for common challenges in structure-based drug discovery. Biomolecular Simulations in Structure-based Drug Discovery is an important resource that: -Contains a review of the current generation of biomolecular simulation tools that have the robustness and speed that allows them to be used as routine tools by non-specialists -Includes information on the novel methods and strategies for the modeling of drug-target interactions within the framework of real-life drug discovery and development -Offers numerous illustrative case studies from a wide-range of therapeutic fields -Presents an application-oriented reference that is ideal for those working in the various fields Written for medicinal chemists, professionals in the pharmaceutical industry, and pharmaceutical chemists, Biomolecular Simulations in Structure-based Drug Discovery is a comprehensive resource to modern simulation tools that complement and have the potential to complement or replace laboratory assays for better results in drug design.