Computational Design of Protein-ligand Interfaces Using RosettaLigand
Author: Brittany Ann Allison
Publisher:
Published: 2016
Total Pages: 140
ISBN-13:
DOWNLOAD EBOOKRead and Download eBook Full
Author: Brittany Ann Allison
Publisher:
Published: 2016
Total Pages: 140
ISBN-13:
DOWNLOAD EBOOKAuthor: Andrew Morin
Publisher:
Published: 2011
Total Pages: 171
ISBN-13:
DOWNLOAD EBOOKAuthor: Barry L. Stoddard
Publisher: Humana
Published: 2016-04-20
Total Pages: 0
ISBN-13: 9781493935673
DOWNLOAD EBOOKThis 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: Sheldon J. Park
Publisher: CRC Press
Published: 2009-09-25
Total Pages: 434
ISBN-13: 1420076590
DOWNLOAD EBOOKExperimental 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
Author: Susanne Eyrisch
Publisher:
Published: 2009
Total Pages:
ISBN-13:
DOWNLOAD EBOOKAuthor: James Devillers
Publisher: CRC Press
Published: 2017-12-15
Total Pages: 479
ISBN-13: 1351647695
DOWNLOAD EBOOKThere is a compelling need for new drugs and efficient treatments against mosquito-borne diseases. Environmentally safe, but effective insecticides that address the problems of resistance are required. Computational Design of Chemicals for the Control of Mosquitoes and Their Diseases explains how the search for new substances effective against mosquitoes and their diseases has benefited from the use of in silico techniques. QSAR modeling is suited to identify the key structural features and/or physicochemical properties explaining an activity and to propose candidate molecules for further evaluation by laboratory tests. Homology modeling is useful to approximate the 3D structure of proteins of interest. Pharmacophore modeling is a powerful means to capture the chemical features responsible for an activity and to identify new potentially active compounds via the virtual screening of databases. Fugacity modeling and a wealth of other modeling paradigms are useful for risk assessment in vector borne disease control.
Author: Shahir Samir Rizk
Publisher:
Published: 2006
Total Pages: 105
ISBN-13: 9780549088127
DOWNLOAD EBOOKThis 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.
Author: Ilan Samish
Publisher: Humana
Published: 2016-12-03
Total Pages: 0
ISBN-13: 9781493966356
DOWNLOAD EBOOKThe 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.
Author: Ta-Yi Yu
Publisher:
Published: 2021
Total Pages: 41
ISBN-13:
DOWNLOAD EBOOKAuthor: M Michael Gromiha
Publisher: World Scientific
Published: 2020-03-05
Total Pages: 424
ISBN-13: 9811211884
DOWNLOAD EBOOKThis 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.