Computational Design Of Ligand Binding Proteins

Author : Barry L. Stoddard
Publisher : Humana
ISBN 13 : 9781493935673
Total Pages : 0 pages
Book Rating : 4.74/5 ( download)

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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.

Author : Robert Stroud
Publisher : Royal Society of Chemistry
ISBN 13 : 1847557961
Total Pages : 400 pages
Book Rating : 4.64/5 ( download)

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Download or read book Computational and Structural Approaches to Drug Discovery written by Robert Stroud and published by Royal Society of Chemistry. This book was released on 2007-10-31 with total page 400 pages. Available in PDF, EPUB and Kindle. Book excerpt: Computational methods impact all aspects of modern drug discovery and most notably these methods move rapidly from academic exercises to becoming drugs in clinical trials... This insightful book represents the experience and understanding of the global experts in the field and spotlights both the structural and medicinal chemistry aspects of drug design. The need to 'encode' the factors that determine adsorption, distribution, metabolism, excretion and toxicology are explored, as they remain the critical issues in this area of research. This indispensable resource provides the reader with: * A rich understanding of modern approaches to docking * A comparison and critical evaluation of state-of-the-art methods * Details on harnessing computational methods for both analysis and prediction * An insight into prediction potencies and protocols for unbiased evaluations of docking and scoring algorithms * Critical reviews of current fragment based methods with perceptive applications to kinases Addressing a wide range of uses of protein structures for drug discovery the Editors have created and essential reference for professionals in the pharmaceutical industry and moreover an indispensable core text for all graduate level courses covering molecular interactions and drug discovery.

Author : Brittany Ann Allison
Publisher :
ISBN 13 :
Total Pages : 140 pages
Book Rating : 4.98/5 ( download)

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Download or read book Computational Design of Protein-ligand Interfaces Using RosettaLigand written by Brittany Ann Allison and published by . This book was released on 2016 with total page 140 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Author : Irena Roterman-Konieczna
Publisher : Springer Science & Business Media
ISBN 13 : 9400752857
Total Pages : 173 pages
Book Rating : 4.56/5 ( download)

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Download or read book Identification of Ligand Binding Site and Protein-Protein Interaction Area written by Irena Roterman-Konieczna and published by Springer Science & Business Media. This book was released on 2012-10-19 with total page 173 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume presents a review of the latest numerical techniques used to identify ligand binding and protein complexation sites. It should be noted that there are many other theoretical studies devoted to predicting the activity of specific proteins and that useful protein data can be found in numerous databases. The aim of advanced computational techniques is to identify the active sites in specific proteins and moreover to suggest a generalized mechanism by which such protein-ligand (or protein-protein) interactions can be effected. Developing such tools is not an easy task – it requires extensive expertise in the area of molecular biology as well as a firm grasp of numerical modeling methods. Thus, it is often viewed as a prime candidate for interdisciplinary research.

Author : Jed W. Pitera
Publisher :
ISBN 13 :
Total Pages : 580 pages
Book Rating : 4.41/5 ( download)

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Download or read book New Computational Methods for Ligand Design written by Jed W. Pitera and published by . This book was released on 1999 with total page 580 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Author : Andrea Bellelli
Publisher : John Wiley & Sons
ISBN 13 : 111923848X
Total Pages : 309 pages
Book Rating : 4.85/5 ( download)

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Download or read book Reversible Ligand Binding written by Andrea Bellelli and published by John Wiley & Sons. This book was released on 2018-01-09 with total page 309 pages. Available in PDF, EPUB and Kindle. Book excerpt: Presents the physical background of ligand binding and instructs on how experiments should be designed and analyzed Reversible Ligand Binding: Theory and Experiment discusses the physical background of protein-ligand interactions—providing a comprehensive view of the various biochemical considerations that govern reversible, as well as irreversible, ligand binding. Special consideration is devoted to enzymology, a field usually treated separately from ligand binding, but actually governed by identical thermodynamic relationships. Attention is given to the design of the experiment, which aids in showing clear evidence of biochemical features that may otherwise escape notice. Classical experiments are reviewed in order to further highlight the importance of the design of the experiment. Overall, the book supplies students with the understanding that is necessary for interpreting ligand binding experiments, formulating plausible reaction schemes, and analyzing the data according to the chosen model(s). Topics covered include: theory of ligand binding to monomeric proteins; practical considerations and commonly encountered problems; oligomeric proteins with multiple binding sites; ligand binding kinetics; hemoglobin and its ligands; single-substrate enzymes and their inhibitors; two-substrate enzymes and their inhibitors; and rapid kinetic methods for studying enzyme reactions. Bridges theory of ligand binding and allostery with experiments Applies historical and physical insight to provide a clear understanding of ligand binding Written by a renowned author with long-standing research and teaching expertise in the area of ligand binding and allostery Based on FEBS Advanced Course lectures on the topic Reversible Ligand Binding: Theory and Experiment is an ideal text reference for students and scientists involved in biophysical chemistry, physical biochemistry, biophysics, molecular biology, protein engineering, drug design, pharmacology, physiology, biotechnology, and bioengineering.

Author : Jiayi Dou
Publisher :
ISBN 13 :
Total Pages : 102 pages
Book Rating : 4.86/5 ( download)

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Download or read book Exploring the Molecular Design of Ligand Binding Sites by Computational Protein Design written by Jiayi Dou and published by . This book was released on 2017 with total page 102 pages. Available in PDF, EPUB and Kindle. Book excerpt: Ligand binding sites in natural proteins, with diverse structural details, provide the foundation for enzymatic activity, antibody-antigen recognition, ligand-induced pathway activation and drug discovery in general. The work presented in this dissertation seeks to understand the general design principles of the molecular details revealed in the ligand-protein complex structures. An engineering approach based on computational protein design was taken to expand the boundary of our current knowledge. By combining computational structural modeling and protein biochemical characterization, computational design of ligand binding proteins iterates between structure-based design hypotheses and experimental validation. This research scheme was applied to two related topics: 1) re-purposing natural ligand binding sites and 2) designing de novo ligand binding proteins. Representative small molecules, steroids (digoxigenin, 17-hydroxylprogesterone, cortisol) and an environmentally sensitive fluorophore (DFHBI), were chosen as design targets. High-resolution X-ray crystal structures of the engineered proteins were obtained and analyzed for modeling feedback. Binding affinity and specificity, protein stability and function, as well as modeling challenges were discussed in each case. The design methods developed and tested in this work represent a systematic way of engineering small molecule binding sites and can be expanded to broad applications. As a rigorous test of our current knowledge, computational design of ligand-binding proteins presented in this work emphasizes the high precision required for accurate ligand positioning and protein conformation modeling.

Author : Andrew Morin
Publisher :
ISBN 13 :
Total Pages : 171 pages
Book Rating : 4.58/5 ( download)

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Download or read book The Computational Design of Protein-ligand Interfaces written by Andrew Morin and published by . This book was released on 2011 with total page 171 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Author : M Michael Gromiha
Publisher : World Scientific
ISBN 13 : 9811211884
Total Pages : 424 pages
Book Rating : 4.81/5 ( download)

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Download or read book Protein Interactions: Computational Methods, Analysis And Applications written by M Michael Gromiha and published by World Scientific. This book was released on 2020-03-05 with total page 424 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Author : Torsten Schwede
Publisher : World Scientific
ISBN 13 : 9814472417
Total Pages : 790 pages
Book Rating : 4.18/5 ( download)

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Download or read book Computational Structural Biology: Methods And Applications written by Torsten Schwede and published by World Scientific. This book was released on 2008-05-02 with total page 790 pages. Available in PDF, EPUB and Kindle. Book excerpt: Computational structural biology has made tremendous progress over the last two decades, and this book provides a recent and broad overview of such computational methods in structural biology. It covers the impact of computational structural biology on protein structure prediction methods, macromolecular function and protein design, and key methods in drug discovery. It also addresses the computational challenges of experimental approaches in structural biology. In addition to reviewing the current state of computational structural biology, each chapter ends with a brief, visionary discussion on the future outlook, whereby the main challenges for the coming years are elucidated. Written by an international panel of expert contributors, this book can serve as a reference manual for students and practitioners alike.