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Protein Modules and Protein-Protein Interactions

Protein Modules and Protein-Protein Interactions
Author:
Publisher: Elsevier
Total Pages: 343
Release: 2002-11-24
Genre: Science
ISBN: 0080493750

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Protein modules engage in a multitude of interactions with one another and with other cellular components, notably with DNA. These interactions are a central aspect of protein function of great relevance in the post-genomic era. This volume describes a panel of approaches for analyzing protein modules and their interactions, ranging from bioinformatics to physical chemistry, to biochemistry, with an emphasis on the structure-function relationship in protein-protein complexes involved in cellular processes including signal transduction. Comprehensive overview of different facets of macromolecule interactions Computational and bioinformatics aspects of analyzing protein modules and their interactions Emphasis on structure-function relationship in protein-protein complexes involved in cellular processes


Modular Protein Domains

Modular Protein Domains
Author: Giovanni Cesareni
Publisher: John Wiley & Sons
Total Pages: 524
Release: 2006-03-06
Genre: Science
ISBN: 3527605894

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Since the full functionality of any given protein can only be understood in terms of its interaction with other, often regulatory proteins, this unique reference source covers all relevant protein domains, including SH2, SH3, PDZ, WW, PTB, EH, PH and PX. Its user-oriented concept combines broad coverage with easy retrieval of essential information, and includes a special section on Web-based tools and databases covering protein modules and functional peptide motifs. Essential for the study of protein-protein interactions in vivo or in silico, and a prerequisite for successful functional proteomics studies. With a prologue by Sir Tom Blundell.


Protein-Protein Interactions

Protein-Protein Interactions
Author: Weibo Cai
Publisher: BoD – Books on Demand
Total Pages: 488
Release: 2012-03-30
Genre: Science
ISBN: 9535103970

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Proteins are indispensable players in virtually all biological events. The functions of proteins are coordinated through intricate regulatory networks of transient protein-protein interactions (PPIs). To predict and/or study PPIs, a wide variety of techniques have been developed over the last several decades. Many in vitro and in vivo assays have been implemented to explore the mechanism of these ubiquitous interactions. However, despite significant advances in these experimental approaches, many limitations exist such as false-positives/false-negatives, difficulty in obtaining crystal structures of proteins, challenges in the detection of transient PPI, among others. To overcome these limitations, many computational approaches have been developed which are becoming increasingly widely used to facilitate the investigation of PPIs. This book has gathered an ensemble of experts in the field, in 22 chapters, which have been broadly categorized into Computational Approaches, Experimental Approaches, and Others.


Protein-Protein Interaction Networks

Protein-Protein Interaction Networks
Author: Stefan Canzar
Publisher: Humana
Total Pages: 0
Release: 2019-10-04
Genre: Science
ISBN: 9781493998722

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This volume explores techniques that study interactions between proteins in different species, and combines them with context-specific data, analysis of omics datasets, and assembles individual interactions into higher-order semantic units, i.e., protein complexes and functional modules. The chapters in this book cover computational methods that solve diverse tasks such as the prediction of functional protein-protein interactions; the alignment-based comparison of interaction networks by SANA; using the RaptorX-ComplexContact webserver to predict inter-protein residue-residue contacts; the docking of alternative confirmations of proteins participating in binary interactions and the visually-guided selection of a docking model using COZOID; the detection of novel functional units by KeyPathwayMiner and how PathClass can use such de novo pathways to classify breast cancer subtypes. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary hardware- and software, step-by-step, readily reproducible computational protocols, and tips on troubleshooting and avoiding known pitfalls. Cutting-edge and comprehensive, Protein-Protein Interaction Networks: Methods and Protocols is a valuable resource for both novice and expert researchers who are interested in learning more about this evolving field.


Molecular Biology of The Cell

Molecular Biology of The Cell
Author: Bruce Alberts
Publisher:
Total Pages: 0
Release: 2002
Genre: Cytology
ISBN: 9780815332183

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Protein-protein Interactions and Networks

Protein-protein Interactions and Networks
Author: Anna Panchenko
Publisher: Springer Science & Business Media
Total Pages: 198
Release: 2010-04-06
Genre: Science
ISBN: 1848001258

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The biological interactions of living organisms, and protein-protein interactions in particular, are astonishingly diverse. This comprehensive book provides a broad, thorough and multidisciplinary coverage of its field. It integrates different approaches from bioinformatics, biochemistry, computational analysis and systems biology to offer the reader a comprehensive global view of the diverse data on protein-protein interactions and protein interaction networks.


Protein Interaction Networks in Health and Disease

Protein Interaction Networks in Health and Disease
Author: Spyros Petrakis
Publisher: Frontiers Media SA
Total Pages: 91
Release: 2016-10-19
Genre: Genetics
ISBN: 2889199827

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The identification and mapping of protein-protein interactions (PPIs) is a major goal in systems biology. Experimental data are currently produced in large scale using a variety of high-throughput assays in yeast or mammalian systems. Analysis of these data using computational tools leads to the construction of large protein interaction networks, which help researchers identify novel protein functions. However, our current view of protein interaction networks is still limited and there is an active field of research trying to further develop this concept to include important processes: the topology of interactions and their changes in real time, the effects of competition for binding to the same protein region, PPI variation due to alternative splicing or post-translational modifications, etc. In particular, a clinically relevant topic for development of the concept of protein interactions networks is the consideration of mutant isoforms, which may be responsible for a pathological condition. Mutations in proteins may result in loss of normal interactions and appearance of novel abnormal interactions that may affect a protein’s function and biological cycle. This Research Topic presents novel findings and recent achievements in the field of protein interaction networks with a focus on disease. Authors describe methods for the identification and quantification of PPIs, the annotation and analysis of networks, considering PPIs and protein complexes formed by mutant proteins associated with pathological conditions or genetic diseases.


Proteins

Proteins
Author: Thomas E. Creighton
Publisher: Macmillan
Total Pages: 534
Release: 1993
Genre: Medical
ISBN: 9780716770305

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Organized on a combined basis of chronology and of structural and functional hierarchy, This comprehensive text describes all aspects of proteins--biosynthesis, evolution, dynamics, ligand binding, catalysis, and energy transduction--not just their structures. This edition (first was 1984) is thoroughly updated--especially in the area of protein biosynthesis--and features end-of-chapter exercises and problems, many of which require the student to consult the cited literature in order to obtain the answer. Annotation copyright by Book News, Inc., Portland, OR


Protein Interactions: Computational Methods, Analysis And Applications

Protein Interactions: Computational Methods, Analysis And Applications
Author: M Michael Gromiha
Publisher: World Scientific
Total Pages: 424
Release: 2020-03-05
Genre: Science
ISBN: 9811211884

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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-protein Complexes

Protein-protein Complexes
Author: Martin Zacharias
Publisher: World Scientific
Total Pages: 401
Release: 2010
Genre: Science
ISBN: 184816338X

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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, etc.) 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.