From Networks To Proteins
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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.
New Approaches Of Protein Function Prediction From Protein Interaction Networks
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Author : Jingyu Hou
language : en
Publisher: Academic Press
Release Date : 2017-01-13
New Approaches Of Protein Function Prediction From Protein Interaction Networks written by Jingyu Hou and has been published by Academic Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2017-01-13 with Mathematics categories.
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
From Networks To Proteins
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Author : Yin Chen
language : en
Publisher:
Release Date : 2011
From Networks To Proteins written by Yin Chen and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2011 with categories.
Abstract: Markov chain and Markov random field (MRF) theory provides a consistent way to model context-dependent entities and correlated features. It is used in conjunction with statistical decision and estimation theories to formulate objective functions in terms of established optimality principles. This dissertation applies MRF modeling and optimization in two areas: network security and protein docking. The first problem is network anomaly detection. The objective is to detect statistically significant temporal or spatial changes in either the underlying process being monitored or the network operation itself. These changes may point to faults, threats, misbehavior, or other anomalies that require intervention. A new statistical anomaly detection framework is introduced that uses Markov models to characterize the "normal" behavior of the network. A series of Markov models are developed, including a node-level model, two tree-indexed models, and a networked Markov chain model to capture temporal and spatial features of network evolution. Large deviations techniques are employed to compare the empirical distribution (estimated from past activity traces) with its most recent empirical measure. Optimal decision rules are developed for each model to identify anomalies in recent activities. Simulation results validate the effectiveness of the proposed anomaly detection algorithms. The second application lies in bioinformatics where the objective is to computationally predict the structure of a complex of two interacting proteins. In the refinement stage of a multi-stage protein docking process, side-chains are extracted from the docking interface and positioned optimally by minimizing an energy function which models interactions among atoms. This combinatorial optimization problem is formulated as a maximum weighted independent set (MWIS) problem. The MWIS problem is NP-hard, yet, the thesis develops a distributed message passing algorithm that can produce effective feasible solutions. The approach is tested on a benchmark of 17 proteins and the results indicate that optimal side-chain positioning significantly improves the binding energy landscape, increasing the correlation between energy and root mean square deviation (RMSD) from the native structure. This new side-chain positioning procedure has the potential to accelerate refinement algorithms seeking very accurate predictions of the native structure and thus serve as an important step in computational docking protocols.
Summarizing Biological Networks
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Author : Sourav S. Bhowmick
language : en
Publisher: Springer
Release Date : 2017-04-17
Summarizing Biological Networks written by Sourav S. Bhowmick and has been published by Springer this book supported file pdf, txt, epub, kindle and other format this book has been release on 2017-04-17 with Computers categories.
This book focuses on the data mining, systems biology, and bioinformatics computational methods that can be used to summarize biological networks. Specifically, it discusses an array of techniques related to biological network clustering, network summarization, and differential network analysis which enable readers to uncover the functional and topological organization hidden in a large biological network. The authors also examine crucial open research problems in this arena. Academics, researchers, and advanced-level students will find this book to be a comprehensive and exceptional resource for understanding computational techniques and their applications for a summary of biological networks.
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.
Towards A Better Understanding Of Protein Protein Interaction Networks
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Author : Tatiana A. Gutiérrez-Bunster
language : en
Publisher:
Release Date : 2014
Towards A Better Understanding Of Protein Protein Interaction Networks written by Tatiana A. Gutiérrez-Bunster and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2014 with categories.
Proteins participate in the majority of cellular processes. To determine the function of a protein it is not sufficient to solely know its sequence, its structure in isolation, or how it works individually. Additionally, we need to know how the protein interacts with other proteins in biological networks. This is because most of the proteins perform their main function through interactions. This thesis sets out to improve the understanding of protein-protein interaction networks (PPINs). For this, we propose three approaches: (1) Studying measures and methods used in social and complex networks. The methods, measures, and properties of social networks allow us to gain an understanding of PPINs via the comparison of different types of network families. We studied models that describe social networks to see which models are useful in describing biological networks. We investigate the similarities and differences in terms of the network community profile and centrality measures. (2) Studying PPINs and their role in evolution. We are interested in the relationship of PPINs and the evolutionary changes between species. We investigate whether the centrality measures are correlated with the variability and similarity in orthologous proteins. (3) Studying protein features that are important to evaluate, classify, and predict interactions. Interactions can be classified according to different characteristics. One characteristic is the energy (that is the attraction or repulsion of the molecules) that occurs in interacting proteins. We identify which type of energy values contributes better to predicting PPIs. We argue that the number of energetic features and their contribution to the interactions can be a key factor in predicting transient and permanent interactions.
The Molecular Chaperones Interaction Networks In Protein Folding And Degradation
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Author : Walid A. Houry
language : en
Publisher: Springer
Release Date : 2014-09-01
The Molecular Chaperones Interaction Networks In Protein Folding And Degradation written by Walid A. Houry and has been published by Springer this book supported file pdf, txt, epub, kindle and other format this book has been release on 2014-09-01 with Science categories.
Molecular chaperones are a fundamental group of proteins that have been identified only relatively recently. They are key components of a protein quality machinery in the cell which insures that the folding process of any newly-synthesized polypeptide chain results in the formation of a properly folded protein and that the folded protein is maintained in an active conformation throughout its functional lifetime. Molecular chaperones have been shown to play essential roles in cell viability under both normal and stress conditions. Chaperones can also assist in the unfolding and degradation of misfolded proteins and in disaggregating preformed protein aggregates. Chaperones are also involved in other cellular functions including protein translocation across membranes, vesicle fusion events, and protein secretion. In recent years, tremendous advances have been made in our understanding of the biology, biochemistry, and biophysics of function of molecular chaperones. In addition, recent technical developments in the fields of proteomics and genomics allowed us to obtain a global view of chaperone interaction networks. Finally, there is now a growing interest in the role of molecular chaperones in diseases. This book will provide a comprehensive analysis of the structure and function of the diverse systems of molecular chaperones and their role in cell stress responses and in diseases from a global network perspective.
Biological Data Mining In Protein Interaction Networks
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Author : Li, Xiao-Li
language : en
Publisher: IGI Global
Release Date : 2009-05-31
Biological Data Mining In Protein Interaction Networks written by Li, Xiao-Li and has been published by IGI Global this book supported file pdf, txt, epub, kindle and other format this book has been release on 2009-05-31 with Technology & Engineering categories.
"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.
Protein Networks And Pathway Analysis
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Author : Yuri Nikolsky
language : en
Publisher: Humana Press
Release Date : 2011-12-01
Protein Networks And Pathway Analysis written by Yuri Nikolsky and has been published by Humana Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2011-12-01 with Science categories.
From the beginning of the OMICs biology era, science has been pursuing the reduction of the complex "genome-wide" assays in order to understand the essential biology that lies beneath it. In Protein Networks and Pathway Analysis, expert practitioners present a compilation of methods of functional data analysis, often referred to as "systems biology," and its applications in drug discovery, medicine and basic disease research. The volume is divided into three convenient sections, covering the elucidation of protein, compound and gene interactions, analytical tools, including networks, interactome and ontologies, and applications of functional analysis. As a volume in the highly successful Methods in Molecular BiologyTM series, this work provides detailed descriptions and hands-on implementation advice. Authoritative and cutting-edge, Protein Networks and Pathway Analysis presents both "wet lab" experimental methods and computational tools in order to cover a broad spectrum of issues in this fascinating new field.
Protein Protein Interactions
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Author : Weibo Cai
language : en
Publisher: BoD – Books on Demand
Release Date : 2012-03-30
Protein Protein Interactions written by Weibo Cai and has been published by BoD – Books on Demand this book supported file pdf, txt, epub, kindle and other format this book has been release on 2012-03-30 with Science categories.
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.