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 Interactions
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Author : M.Michael Gromiha
language : en
Publisher: World Scientific Publishing Company
Release Date : 2020-03-05
Protein Interactions written by M.Michael Gromiha and has been published by World Scientific Publishing Company this book supported file pdf, txt, epub, kindle and other format this book has been release on 2020-03-05 with Protein-protein interactions categories.
The 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.
Principles Of Computational Cell Biology
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Author : Volkhard Helms
language : en
Publisher: John Wiley & Sons
Release Date : 2019-04-29
Principles Of Computational Cell Biology written by Volkhard Helms and has been published by John Wiley & Sons this book supported file pdf, txt, epub, kindle and other format this book has been release on 2019-04-29 with Medical categories.
Computational cell biology courses are increasingly obligatory for biology students around the world but of course also a must for mathematics and informatics students specializing in bioinformatics. This book, now in its second edition is geared towards both audiences. The author, Volkhard Helms, has, in addition to extensive teaching experience, a strong background in biology and informatics and knows exactly what the key points are in making the book accessible for students while still conveying in depth knowledge of the subject.About 50% of new content has been added for the new edition. Much more room is now given to statistical methods, and several new chapters address protein-DNA interactions, epigenetic modifications, and microRNAs.
Protein Protein And Domain Domain Interactions
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Author : Pandjassarame Kangueane
language : en
Publisher: Springer
Release Date : 2018-02-16
Protein Protein And Domain Domain Interactions written by Pandjassarame Kangueane and has been published by Springer this book supported file pdf, txt, epub, kindle and other format this book has been release on 2018-02-16 with Medical categories.
This book illustrates the importance and significance of the molecular (physical and chemical) and evolutionary (gene fusion) principles of protein-protein and domain-domain interactions towards the understanding of cell division, disease mechanism and target definition in drug discovery. It describes the complex issues associated with this phenomenon using cutting edge advancement in Bioinformatics and Bioinformation Discovery. The chapters provide current information pertaining to the types of protein-protein complexes (homodimers, heterodimers, multimer complexes) in context with various specific and sensitive biological functions. The significance of such complex formation in human biology in the light of molecular evolution is also highlighted using several examples. The chapters also describe recent advancements on the molecular principles of protein-protein interaction with reference to evolution towards target identification in drug discovery. Finally, the book also elucidates a comprehensive yet a representative description of a large number of challenges associated with the molecular interaction of proteins.
Protein Protein Recognition
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Author : Colin Kleanthous
language : en
Publisher: Oxford University Press, USA
Release Date : 2000
Protein Protein Recognition written by Colin Kleanthous and has been published by Oxford University Press, USA this book supported file pdf, txt, epub, kindle and other format this book has been release on 2000 with Science categories.
The purpose of Protein-Protein Recognition is to bring together concepts and systems pertaining to protein-protein interactions in a single unifying volume. In the light of the information from the genome sequencing projects and the increase in structural information it is an opportune time to try to make generalizations about how and why proteins form complexes with each other. The emphasis of the book is on heteromeric complexes (complexes in which each of the components can exist in an unbound state) and will use well-studied model systems to explain the processes of forming complexes. After an introductory section on the kinetics, thermodynamics, analysis, and classification of protein-protein interactions, weak, intermediate, and high affinity complexes are dealt with in turn. Weak affinity complexes are represented by electron transfer proteins and integrin complexes. Anti-lysozyme antibodies, the MHC proteins and their interactions with T-cell receptors, and the protein interactions of eukaryotic signal transduction are the systems used to explain complexes with intermediate affinities. Finally, tight binding complexes are represented by the interaction of protein inhibitors with serine proteases and by nuclease inhibitor complexes. Throughout the chapters common themes are the technologies which have had the greatest impact, how specificity is determined, how complexes are stabilized, and medical and industrial applications.
Advances In Protein Molecular And Structural Biology Methods
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Author : Timir Tripathi
language : en
Publisher: Academic Press
Release Date : 2022-01-14
Advances In Protein Molecular And Structural Biology Methods written by Timir Tripathi and has been published by Academic Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2022-01-14 with Science categories.
Advances in Protein Molecular and Structural Biology Methods offers a complete overview of the latest tools and methods applicable to the study of proteins at the molecular and structural level. The book begins with sections exploring tools to optimize recombinant protein expression and biophysical techniques such as fluorescence spectroscopy, NMR, mass spectrometry, cryo-electron microscopy, and X-ray crystallography. It then moves towards computational approaches, considering structural bioinformatics, molecular dynamics simulations, and deep machine learning technologies. The book also covers methods applied to intrinsically disordered proteins (IDPs)followed by chapters on protein interaction networks, protein function, and protein design and engineering. It provides researchers with an extensive toolkit of methods and techniques to draw from when conducting their own experimental work, taking them from foundational concepts to practical application. - Presents a thorough overview of the latest and emerging methods and technologies for protein study - Explores biophysical techniques, including nuclear magnetic resonance, X-ray crystallography, and cryo-electron microscopy - Includes computational and machine learning methods - Features a section dedicated to tools and techniques specific to studying intrinsically disordered proteins
Computational Intelligence And Bioinformatics
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Author : De-Shuang Huang
language : en
Publisher: Springer Science & Business Media
Release Date : 2006-08-03
Computational Intelligence And Bioinformatics written by De-Shuang Huang 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 2006-08-03 with Computers categories.
This book constitutes the refereed proceedings of the International Conference on Intelligent Computing, ICIC 2006, held in Kunming, China, in August 2006. The book presents 165 revised full papers, carefully reviewed. Topics covered include ant colony optimization, particle swarm optimization, swarm intelligence, autonomy-oriented computing, quantum and molecular computations, biological and DNA computing, intelligent computing in bioinformatics, intelligent computing in computational biology and drug design, computational genomics and proteomics, and more.
Clinical Technologies Concepts Methodologies Tools And Applications
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Author : Management Association, Information Resources
language : en
Publisher: IGI Global
Release Date : 2011-05-31
Clinical Technologies Concepts Methodologies Tools And Applications written by Management Association, Information Resources and has been published by IGI Global this book supported file pdf, txt, epub, kindle and other format this book has been release on 2011-05-31 with Medical categories.
"This multi-volume book delves into the many applications of information technology ranging from digitizing patient records to high-performance computing, to medical imaging and diagnostic technologies, and much more"--
Machine Learning Under Resource Constraints Applications
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Author : Katharina Morik
language : en
Publisher: Walter de Gruyter GmbH & Co KG
Release Date : 2022-12-31
Machine Learning Under Resource Constraints Applications written by Katharina Morik and has been published by Walter de Gruyter GmbH & Co KG this book supported file pdf, txt, epub, kindle and other format this book has been release on 2022-12-31 with Science categories.
Machine Learning under Resource Constraints addresses novel machine learning algorithms that are challenged by high-throughput data, by high dimensions, or by complex structures of the data in three volumes. Resource constraints are given by the relation between the demands for processing the data and the capacity of the computing machinery. The resources are runtime, memory, communication, and energy. Hence, modern computer architectures play a significant role. Novel machine learning algorithms are optimized with regard to minimal resource consumption. Moreover, learned predictions are executed on diverse architectures to save resources. It provides a comprehensive overview of the novel approaches to machine learning research that consider resource constraints, as well as the application of the described methods in various domains of science and engineering. Volume 3 describes how the resource-aware machine learning methods and techniques are used to successfully solve real-world problems. The book provides numerous specific application examples. In the areas of health and medicine, it is demonstrated how machine learning can improve risk modelling, diagnosis, and treatment selection for diseases. Machine learning supported quality control during the manufacturing process in a factory allows to reduce material and energy cost and save testing times is shown by the diverse real-time applications in electronics and steel production as well as milling. Additional application examples show, how machine-learning can make traffic, logistics and smart cities more effi cient and sustainable. Finally, mobile communications can benefi t substantially from machine learning, for example by uncovering hidden characteristics of the wireless channel.
Research In Computational Molecular Biology
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Author : Serafim Batzoglou
language : en
Publisher: Springer Science & Business Media
Release Date : 2009-05-04
Research In Computational Molecular Biology written by Serafim Batzoglou 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 2009-05-04 with Computers categories.
This book constitutes the refereed proceedings of the 13th Annual International Conference on Research in Computational Molecular Biology, RECOMB 2009, held in Tucson, Arisona, USA in May 2009. The 37 revised full papers presented were carefully reviewed and selected from 166 submissions. As the top conference in computational molecular biology, RECOMB addresses all current issues in algorithmic, theoretical, and experimental bioinformatics such as molecular sequence analysis, recognition of genes and regulatory elements, molecular evolution, protein structure, structural genomics, gene expression, gene networks, drug design, combinatorial libraries, computational proteomics, as well as structural and functional genomics.