Computational Prediction Of Protein Complexes From Protein Interaction Networks
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Computational Prediction Of Protein Complexes From Protein Interaction Networks
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Author : Sriganesh Srihari
language : en
Publisher: Morgan & Claypool
Release Date : 2017-05-30
Computational Prediction Of Protein Complexes From Protein Interaction Networks written by Sriganesh Srihari and has been published by Morgan & Claypool this book supported file pdf, txt, epub, kindle and other format this book has been release on 2017-05-30 with Science categories.
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.
Protein Protein Interactions And Networks
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Author : Anna Panchenko
language : en
Publisher: Springer Science & Business Media
Release Date : 2010-04-06
Protein Protein Interactions And Networks written by Anna Panchenko and has been published by Springer Science & Business Media this book supported file pdf, txt, epub, kindle and other format this book has been release on 2010-04-06 with Science categories.
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 Protein Interaction Networks
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Author : Stefan Canzar
language : en
Publisher: Humana
Release Date : 2019-10-04
Protein Protein Interaction Networks written by Stefan Canzar and has been published by Humana this book supported file pdf, txt, epub, kindle and other format this book has been release on 2019-10-04 with Science categories.
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.
Protein Interaction Networks
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Author : Aidong Zhang
language : en
Publisher: Cambridge University Press
Release Date : 2009-04-06
Protein Interaction Networks written by Aidong Zhang and has been published by Cambridge University Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2009-04-06 with Computers categories.
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.
Protein Protein Interactions And Networks
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Author : Anna Panchenko
language : en
Publisher: Springer
Release Date : 2009-08-29
Protein Protein Interactions And Networks written by Anna Panchenko and has been published by Springer this book supported file pdf, txt, epub, kindle and other format this book has been release on 2009-08-29 with Science categories.
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 Interactions Computational Methods Analysis And Applications
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Author : M Michael Gromiha
language : en
Publisher: World Scientific
Release Date : 2020-03-05
Protein Interactions Computational Methods Analysis And Applications written by M Michael Gromiha and has been published by World Scientific this book supported file pdf, txt, epub, kindle and other format this book has been release on 2020-03-05 with Science categories.
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.
Computational Protein Protein Interactions
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Author : Ruth Nussinov
language : en
Publisher: CRC Press
Release Date : 2009-06-26
Computational Protein Protein Interactions written by Ruth Nussinov and has been published by CRC Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2009-06-26 with Science categories.
Often considered the workhorse of the cellular machinery, proteins are responsible for functions ranging from molecular motors to signaling. The broad recognition of their involvement in all cellular processes has led to focused efforts to predict their functions from sequences, and if available, from their structures. An overview of current resear
Protein Protein Interactions
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Author : Krishna Mohan Poluri
language : en
Publisher: Springer Nature
Release Date : 2021-05-19
Protein Protein Interactions written by Krishna Mohan Poluri and has been published by Springer Nature this book supported file pdf, txt, epub, kindle and other format this book has been release on 2021-05-19 with Science categories.
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.
Proteomics And Protein Protein Interactions
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Author : Gabriel Waksman
language : en
Publisher: Springer Science & Business Media
Release Date : 2005-12-21
Proteomics And Protein Protein Interactions written by Gabriel Waksman and has been published by Springer Science & Business Media this book supported file pdf, txt, epub, kindle and other format this book has been release on 2005-12-21 with Medical categories.
The rapidly evolving field of protein science has now come to realize the ubiquity and importance of protein-protein interactions. It had been known for some time that proteins may interact with each other to form functional complexes, but it was thought to be the property of only a handful of key proteins. However, with the advent of high throughput proteomics to monitor protein-protein interactions at an organism level, we can now safely state that protein-protein interactions are the norm and not the exception. Thus, protein function must be understood in the larger context of the various binding complexes that each protein may form with interacting partners at a given time in the life cycle of a cell. Proteins are now seen as forming sophisticated interaction networks subject to remarkable regulation. The study of these interaction networks and regulatory mechanism, which I would like to term "systems proteomics," is one of the thriving fields of proteomics. The bird-eye view that systems proteomics offers should not however mask the fact that proteins are each characterized by a unique set of physical and chemical properties. In other words, no protein looks and behaves like another. This complicates enormously the design of high-throughput proteomics methods. Unlike genes, which, by and large, display similar physico-chemical behaviors and thus can be easily used in a high throughput mode, proteins are not easily amenable to the same treatment. It is thus important to remind researchers active in the proteomics field the fundamental basis of protein chemistry. This book attempts to bridge the two extreme ends of protein science: on one end, systems proteomics, which describes, at a system level, the intricate connection network that proteins form in a cell, and on the other end, protein chemistry and biophysics, which describe the molecular properties of individual proteins and the structural and thermodynamic basis of their interactions within the network. Bridging the two ends of the spectrum is bioinformatics and computational chemistry. Large data sets created by systems proteomics need to be mined for meaningful information, methods need to be designed and implemented to improve experimental designs, extract signal over noise, and reject artifacts, and predictive methods need to be worked out and put to the test. Computational chemistry faces similar challenges. The prediction of binding thermodynamics of protein-protein interaction is still in its infancy. Proteins are large objects, and simplifying assumptions and shortcuts still need to be applied to make simulations manageable, and this despite exponential progress in computer technology. Finally, the study of proteins impacts directly on human health. It is an obvious statement to say that, for decades, enzymes, receptors, and key regulator proteins have been targeted for drug discovery. However, a recent and exciting development is the exploitation of our knowledge of protein-protein interaction for the design of new pharmaceuticals. This presents particular challenges because protein-protein interfaces are generally shallow and interactions are weak. However, progress is clearly being made and the book seeks to provide examples of successes in this area.
Special Protein Molecules Computational Identification
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Author : Quan Zou
language : en
Publisher: MDPI
Release Date : 2018-08-09
Special Protein Molecules Computational Identification written by Quan Zou and has been published by MDPI this book supported file pdf, txt, epub, kindle and other format this book has been release on 2018-08-09 with Electronic books categories.
This book is a printed edition of the Special Issue "Special Protein Molecules Computational Identification" that was published in IJMS