Computer Simulations of Protein Structures and Interactions
Computer Simulations of Protein Structures and Interactions

Author: Serafin Fraga

Publisher: Springer Science & Business Media

Published: 2013-04-17

Total Pages: 296

ISBN-13: 3642514995

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Protein engineering endeavors to design new peptides and proteins or to change the structural and/or functional characteristics of existing ones for specific purposes, opening the way for the development of new drugs. This work develops in a comprehensive way the theoretical formulation for the methods used in computer-assisted modeling and predictions, starting from the basic concepts and proceeding to the more sophisticated methods, such as Monte Carlo and molecular dynamics. An evaluation of the approximations inherent to the simulations will allow the reader to obtain a perspective of the possible deficiencies and difficulties and approach the task with realistic expectations. Examples from the authors laboratories, as well as from the literature provide useful information.

Peptide Bionanomaterials
Peptide Bionanomaterials

Author: Mohamed A. Elsawy

Publisher: Springer Nature

Published: 2023-08-28

Total Pages: 556

ISBN-13: 3031293606

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Molecular self-assembly has been exploited by nature for developing the higher functional macromolecular structures of both the genome and proteome. Inspired by nature, there has been a surge of research, in the last two decades, for the molecular engineering of peptide-based self-assembling nanostructures, adopting the bottom-up design approach. This book gives the reader an overview on the design rules for de novo self-assembling peptide and reviews the diverse range of bioinspired peptide nanostructures such as β-sheet and β-hairpin, α-helical and coiled coil, self-assembling short peptides and peptidomimetics, collagen-based and elastin-like peptides, silk peptides, peptide amphiphiles, peptides co-polymers and others. The book also covers the wide variety of responsive and functional biomaterials that have been innovated based on those nanostructures for various applications ranging from tissue engineering, therapeutics and drug delivery to antimicrobial nanomaterials and biosensors. Finally, the book also discusses the peptide bionanomaterials global market and the future of the emerging industry. Chapter “Characterization of Peptide-Based Nanomaterials” is available open access under a Creative Commons Attribution 4.0 International License via link.springer.com.

Dancing protein clouds: Intrinsically disordered proteins in health and disease, Part A
Dancing protein clouds: Intrinsically disordered proteins in health and disease, Part A

Author:

Publisher: Academic Press

Published: 2019-09-12

Total Pages: 426

ISBN-13: 012816851X

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"Dancing protein clouds: Intrinsically disordered proteins in the norm and pathology" represents a set of selected studies on a variety of research topics related to intrinsically disordered proteins. Topics in this update include structural and functional characterization of several important intrinsically disordered proteins, such as 14-3-3 proteins and their partners, as well as proteins from muscle sarcomere; representation of intrinsic disorder-related concept of protein structure-function continuum; discussion of the role of intrinsic disorder in phenotypic switching; consideration of the role of intrinsically disordered proteins in the pathogenesis of neurodegenerative diseases and cancer; discussion of the roles of intrinsic disorder in functional amyloids; demonstration of the usefulness of the analysis of translational diffusion of unfolded and intrinsically disordered proteins; consideration of various computational tools for evaluation of functions of intrinsically disordered regions; and discussion of the role of shear stress in the amyloid formation of intrinsically disordered regions in the brain.

Biomimetic Materials And Design
Biomimetic Materials And Design

Author: Angela Dillow

Publisher: CRC Press

Published: 2002-08-28

Total Pages: 704

ISBN-13: 9780203908976

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Detailing techniques in wound healing and reconstruction, this reference describes the mechanisms and architecture of biological systems to formulate and design natural and synthetic compounds, degradable and non-degradable scaffolds, and targeted drug delivery devices. It offers strategies to control adhesive interactions, elicit specific cellular responses, and improve the biocompatibility, performance, and durability of prosthetic materials. Covering advances in the field, the book discusses the effect of topographical features on cell behaviors such as orientation, adhesion, migration, proliferation, and differentation.

Computational Design of Ligand Binding Proteins
Computational Design of Ligand Binding Proteins

Author: Barry L. Stoddard

Publisher: Humana

Published: 2016-04-20

Total Pages: 0

ISBN-13: 9781493935673

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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.

Data Mining
Data Mining

Author: Florin Gorunescu

Publisher: Springer Science & Business Media

Published: 2011-03-10

Total Pages: 364

ISBN-13: 3642197213

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The knowledge discovery process is as old as Homo sapiens. Until some time ago this process was solely based on the ‘natural personal' computer provided by Mother Nature. Fortunately, in recent decades the problem has begun to be solved based on the development of the Data mining technology, aided by the huge computational power of the 'artificial' computers. Digging intelligently in different large databases, data mining aims to extract implicit, previously unknown and potentially useful information from data, since “knowledge is power”. The goal of this book is to provide, in a friendly way, both theoretical concepts and, especially, practical techniques of this exciting field, ready to be applied in real-world situations. Accordingly, it is meant for all those who wish to learn how to explore and analysis of large quantities of data in order to discover the hidden nugget of information.

Computational Protein Design
Computational Protein Design

Author: Ilan Samish

Publisher: Humana

Published: 2016-12-03

Total Pages: 0

ISBN-13: 9781493966356

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The 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.