The Computational Design Of Protein Ligand Interfaces
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Computational Design Of Protein Ligand Interfaces Using Rosettaligand
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Author : Brittany Ann Allison
language : en
Publisher:
Release Date : 2016
Computational Design Of Protein Ligand Interfaces Using Rosettaligand written by Brittany Ann Allison and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2016 with Electronic dissertations categories.
The Computational Design Of Protein Ligand Interfaces
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Author : Andrew Morin
language : en
Publisher:
Release Date : 2011
The Computational Design Of Protein Ligand Interfaces written by Andrew Morin and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2011 with Biological interfaces categories.
Computational Design Of Ligand Binding Proteins
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Author : Barry L. Stoddard
language : en
Publisher: Humana
Release Date : 2016-04-20
Computational Design Of Ligand Binding Proteins written by Barry L. Stoddard and has been published by Humana this book supported file pdf, txt, epub, kindle and other format this book has been release on 2016-04-20 with Science categories.
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.
Computational Intelligence In Protein Ligand Interaction Analysis
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Author : Bing Wang
language : en
Publisher: Academic Press
Release Date : 2024-03-22
Computational Intelligence In Protein Ligand Interaction Analysis written by Bing Wang and has been published by Academic Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2024-03-22 with Science categories.
Computational Intelligence in Protein-Ligand Interaction Analysis presents computational techniques for predicting protein-ligand interactions, recognizing protein interaction sites, and identifying protein drug targets. The book emphasizes novel approaches to protein-ligand interactions, including machine learning and deep learning, presenting a state-of-the-art suite of skills for researchers. The volume represents a resource for scientists, detailing the fundamentals of computational methods, showing how to use computational algorithms to study protein interaction data, and giving scientific explanations for biological data through computational intelligence. Fourteen chapters offer a comprehensive guide to protein interaction data and computational intelligence methods for protein-ligand interactions. Presents a guide to computational techniques for protein-ligand interaction analysis Guides researchers in developing advanced computational intelligence methods for the protein-ligand problem Identifies appropriate computational tools for various problems Demonstrates the use of advanced techniques such as vector machine, neural networks, and machine learning Offers the computational, mathematical and statistical skills researchers need
Protein Interactions Computational Methods Analysis And Applications
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Author : M Michael Gromiha
language : en
Publisher: World Scientific
Release Date : 2020-03-05
Protein Interactions Computational Methods Analysis And Applications written by M Michael Gromiha and has been published by World Scientific this book supported file pdf, txt, epub, kindle and other format this book has been release on 2020-03-05 with Science categories.
This book is indexed in Chemical Abstracts ServiceThe interactions of proteins with other molecules are important in many cellular activities. Investigations have been carried out to understand the recognition mechanism, identify the binding sites, analyze the the binding affinity of complexes, and study the influence of mutations on diseases. Protein interactions are also crucial in structure-based drug design.This book covers computational analysis of protein-protein, protein-nucleic acid and protein-ligand interactions and their applications. It provides up-to-date information and the latest developments from experts in the field, using illustrations to explain the key concepts and applications. This volume can serve as a single source on comparative studies of proteins interacting with proteins/DNAs/RNAs/carbohydrates and small molecules.
Protein Engineering And Design
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Author : Sheldon J. Park
language : en
Publisher: CRC Press
Release Date : 2009-09-25
Protein Engineering And Design written by Sheldon J. Park and has been published by CRC Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2009-09-25 with Medical categories.
Experimental protein engineering and computational protein design are broad but complementary strategies for developing proteins with altered or novel structural properties and biological functions. By describing cutting-edge advances in both of these fields, Protein Engineering and Design aims to cultivate a synergistic approach to protein science
Protein Ligand Interactions
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Author : Holger Gohlke
language : en
Publisher: John Wiley & Sons
Release Date : 2012-04-06
Protein Ligand Interactions written by Holger Gohlke and has been published by John Wiley & Sons this book supported file pdf, txt, epub, kindle and other format this book has been release on 2012-04-06 with Medical categories.
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.
Computational Design Of Protein Ligand Interactions Experiments And Applications
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Author : Shahir Samir Rizk
language : en
Publisher:
Release Date : 2006
Computational Design Of Protein Ligand Interactions Experiments And Applications written by Shahir Samir Rizk and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2006 with Protein engineering categories.
This work describes the application of engineering protein-ligand interactions to the design of biosensors and multisensors. Structure-based computational design was used to engineer a zinc binding site in the enzyme ATPase. As a result, zinc acts as an allosteric regulator of the enzymatic activity. Computational design was further applied to the redesign of the binding specificity of glucose- and ribose binding proteins to bind pinacolymethylphosphonic acid (PMPA), a degradation product of the nerve agent soman. The computationally redesigned binding proteins were labeled with a thiolreactive fluorophore at a unique cysteine position and as a result, a change in fluorescence is exhibited by the protein-fluorophore conjugate in response to ligand binding. The results demonstrate that the engineered proteins act as reagentless fluorescent biosensors for PMPA and exhibit a range of affinities between 0.045 and 10 muM. Protein engineering techniques were used to extent the ability of a single biosensor element to distinguish between several similar target ligands by incorporating many sensor elements in a multisensor system. The protein PhnD, a periplasmic binding protein that binds many phosphonates, was characterized, and variants were constructed by introducing point mutations in its binding pocket. The PhnD variants exhibit differential binding affinities to several similar molecules and were used as sensor elements in a fluorescent multisensor system. The multisensor can be used to determine the concentrations of many analytes in a solution and can detect the presence of an interferent for which it has not been characterized by taking advantage of the non-linear nature of the fluorescent response to ligand binding.
Methods In Protein Design
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Author :
language : en
Publisher: Academic Press
Release Date : 2013-02-14
Methods In Protein Design written by and has been published by Academic Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2013-02-14 with Science categories.
This new volume of Methods in Enzymology continues the legacy of this premier serial by containing quality chapters authored by leaders in the field. This volume covers methods in protein design and it has chapters on such topics as protein switch engineering by domain insertion, evolution based design of proteins, and computationally designed proteins. Continues the legacy of this premier serial with quality chapters authored by leaders in the field Covers methods in protein design Contains chapters with such topics as protein switch engineering by domain insertion, evolution-based design of proteins, and computationally designed proteins
Protein Protein Complexes
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Author : Martin Zacharias
language : en
Publisher: World Scientific
Release Date : 2010
Protein Protein Complexes written by Martin Zacharias and has been published by World Scientific this book supported file pdf, txt, epub, kindle and other format this book has been release on 2010 with Medical categories.
Given the immense progress achieved in elucidating protein-protein complex structures and in the field of protein interaction modeling, there is great demand for a book that gives interested researchers/students a comprehensive overview of the field. This book does just that. It focuses on what can be learned about protein-protein interactions from the analysis of protein-protein complex structures and interfaces. What are the driving forces for protein-protein association? How can we extract the mechanism of specific recognition from studying protein-protein interfaces? How can this knowledge be used to predict and design protein-protein interactions (interaction regions and complex structures)? What methods are currently employed to design protein-protein interactions, and how can we influence protein-protein interactions by mutagenesis and small-molecule drugs or peptide mimetics?The book consists of about 15 review chapters, written by experts, on the characterization of protein-protein interfaces, structure determination of protein complexes (by NMR and X-ray), theory of protein-protein binding, dynamics of protein interfaces, bioinformatics methods to predict interaction regions, and prediction of protein-protein complex structures (docking and homology modeling of complexes, etcetera.) and design of protein-protein interactions. It serves as a bridge between studying/analyzing protein-protein complex structures (interfaces), predicting interactions, and influencing/designing interactions.