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BOOK EXCERPT:
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.
Product Details :
Genre |
: Science |
Author |
: Anna Panchenko |
Publisher |
: Springer Science & Business Media |
Release |
: 2010-04-06 |
File |
: 198 Pages |
ISBN-13 |
: 9781848001251 |
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BOOK EXCERPT:
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.
Product Details :
Genre |
: Science |
Author |
: Weibo Cai |
Publisher |
: BoD – Books on Demand |
Release |
: 2012-03-30 |
File |
: 488 Pages |
ISBN-13 |
: 9789535103974 |
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BOOK EXCERPT:
This book provides a comprehensive overview of the fundamental aspects of protein-protein interactions (PPI), including a detailed account of the energetics and thermodynamics involved in these interactions. It also discusses a number of computational and experimental approaches for the prediction of PPI interactions and reviews their principles, advantages, drawbacks, and the recent developments. Further, it offers structural and mechanistic insights into the formation of protein-protein complexes and maps different PPIs into networks to delineate various pathways that operate at the cellular level. Lastly, it describes computational protein-protein docking techniques and discusses their implications for further experimental research. Given its scope, this book is a valuable resource for students, researchers, scientists, entrepreneurs, and medical/healthcare professionals.
Product Details :
Genre |
: Science |
Author |
: Krishna Mohan Poluri |
Publisher |
: Springer Nature |
Release |
: 2021-05-19 |
File |
: 346 Pages |
ISBN-13 |
: 9789811615948 |
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BOOK EXCERPT:
This detailed volume provides a comprehensive collection of classic and cutting-edge methods and techniques in mapping protein-protein interactions. The chapters include a variety of in vitro and in vivo experimental methods covering cell biology, biochemistry, and biophysics. In addition, the book also explores in silico methods including sequence-, structure-, and phylogenetic profile-based approaches as well as gene expression and machine learning methods. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step and readily reproducible laboratory protocols, as well as tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Protein-Protein Interactions: Methods and Protocols serves as an ideal guide for researchers working in protein science and beyond.
Product Details :
Genre |
: Science |
Author |
: Shahid Mukhtar |
Publisher |
: Springer Nature |
Release |
: 2023-07-14 |
File |
: 480 Pages |
ISBN-13 |
: 9781071633274 |
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BOOK EXCERPT:
The analysis of protein-protein interactions is fundamental to the understanding of cellular organization, processes, and functions. Proteins seldom act as single isolated species; rather, proteins involved in the same cellular processes often interact with each other. Functions of uncharacterized proteins can be predicted through comparison with the interactions of similar known proteins. Recent large-scale investigations of protein-protein interactions using such techniques as two-hybrid systems, mass spectrometry, and protein microarrays have enriched the available protein interaction data and facilitated the construction of integrated protein-protein interaction networks. The resulting large volume of protein-protein interaction data has posed a challenge to experimental investigation. This book provides a comprehensive understanding of the computational methods available for the analysis of protein-protein interaction networks. It offers an in-depth survey of a range of approaches, including statistical, topological, data-mining, and ontology-based methods. The author discusses the fundamental principles underlying each of these approaches and their respective benefits and drawbacks, and she offers suggestions for future research.
Product Details :
Genre |
: Computers |
Author |
: Aidong Zhang |
Publisher |
: Cambridge University Press |
Release |
: 2009-04-06 |
File |
: 283 Pages |
ISBN-13 |
: 9781139479035 |
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BOOK EXCERPT:
"The goal of this book is to disseminate research results and best practices from cross-disciplinary researchers and practitioners interested in, and working on bioinformatics, data mining, and proteomics"--Provided by publisher.
Product Details :
Genre |
: Technology & Engineering |
Author |
: Li, Xiao-Li |
Publisher |
: IGI Global |
Release |
: 2009-05-31 |
File |
: 450 Pages |
ISBN-13 |
: 9781605663999 |
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BOOK EXCERPT:
Product Details :
Genre |
: Science |
Author |
: Gorka Lasso Cabrera |
Publisher |
: Frontiers Media SA |
Release |
: 2022-08-02 |
File |
: 121 Pages |
ISBN-13 |
: 9782889766147 |
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BOOK EXCERPT:
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.
Product Details :
Genre |
: Genetics |
Author |
: Spyros Petrakis |
Publisher |
: Frontiers Media SA |
Release |
: 2016-10-19 |
File |
: 91 Pages |
ISBN-13 |
: 9782889199822 |
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BOOK EXCERPT:
Complexes of physically interacting proteins constitute fundamental functional units that drive almost all biological processes within cells. A faithful reconstruction of the entire set of protein complexes (the "complexosome") is therefore important not only to understand the composition of complexes but also the higher level functional organization within cells. Advances over the last several years, particularly through the use of high-throughput proteomics techniques, have made it possible to map substantial fractions of protein interactions (the "interactomes") from model organisms including Arabidopsis thaliana (a flowering plant), Caenorhabditis elegans (a nematode), Drosophila melanogaster (fruit fly), and Saccharomyces cerevisiae (budding yeast). These interaction datasets have enabled systematic inquiry into the identification and study of protein complexes from organisms. Computational methods have played a significant role in this context, by contributing accurate, efficient, and exhaustive ways to analyze the enormous amounts of data. These methods have helped to compensate for some of the limitations in experimental datasets including the presence of biological and technical noise and the relative paucity of credible interactions. In this book, we systematically walk through computational methods devised to date (approximately between 2000 and 2016) for identifying protein complexes from the network of protein interactions (the protein-protein interaction (PPI) network). We present a detailed taxonomy of these methods, and comprehensively evaluate them for protein complex identification across a variety of scenarios including the absence of many true interactions and the presence of false-positive interactions (noise) in PPI networks. Based on this evaluation, we highlight challenges faced by the methods, for instance in identifying sparse, sub-, or small complexes and in discerning overlapping complexes, and reveal how a combination of strategies is necessary to accurately reconstruct the entire complexosome.
Product Details :
Genre |
: Science |
Author |
: Sriganesh Srihari |
Publisher |
: Morgan & Claypool |
Release |
: 2017-05-30 |
File |
: 259 Pages |
ISBN-13 |
: 9781970001549 |
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BOOK EXCERPT:
New Approaches of Protein Function Prediction from Protein Interaction Networks contains the critical aspects of PPI network based protein function prediction, including semantically assessing the reliability of PPI data, measuring the functional similarity between proteins, dynamically selecting prediction domains, predicting functions, and establishing corresponding prediction frameworks. Functional annotation of proteins is vital to biological and clinical research and other applications due to the important roles proteins play in various biological processes. Although the functions of some proteins have been annotated via biological experiments, there are still many proteins whose functions are yet to be annotated due to the limitations of existing methods and the high cost of experiments. To overcome experimental limitations, this book helps users understand the computational approaches that have been rapidly developed for protein function prediction. Provides innovative approaches and new developments targeting key issues in protein function prediction Presents heuristic ideas for further research in this challenging area
Product Details :
Genre |
: Mathematics |
Author |
: Jingyu Hou |
Publisher |
: Academic Press |
Release |
: 2017-01-13 |
File |
: 126 Pages |
ISBN-13 |
: 9780128099445 |