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New Approaches of Protein Function Prediction from Protein Interaction Networks

New Approaches of Protein Function Prediction from Protein Interaction Networks
A Book

by Jingyu Hou

  • Publisher : Academic Press
  • Release : 2017-01-13
  • Pages : 124
  • ISBN : 0128099445
  • Language : En, Es, Fr & De
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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

Protein Interaction Networks

Protein Interaction Networks
Computational Analysis

by Aidong Zhang

  • Publisher : Cambridge University Press
  • Release : 2009-04-06
  • Pages : 278
  • ISBN : 0521888956
  • Language : En, Es, Fr & De
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The first full survey of statistical, topological, data-mining, and ontology-based methods for analyzing protein-protein interaction networks.

Protein Function Prediction for Omics Era

Protein Function Prediction for Omics Era
A Book

by Daisuke Kihara

  • Publisher : Springer Science & Business Media
  • Release : 2011-04-19
  • Pages : 310
  • ISBN : 9789400708815
  • Language : En, Es, Fr & De
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Gene function annotation has been a central question in molecular biology. The importance of computational function prediction is increasing because more and more large scale biological data, including genome sequences, protein structures, protein-protein interaction data, microarray expression data, and mass spectrometry data, are awaiting biological interpretation. Traditionally when a genome is sequenced, function annotation of genes is done by homology search methods, such as BLAST or FASTA. However, since these methods are developed before the genomics era, conventional use of them is not necessarily most suitable for analyzing a large scale data. Therefore we observe emerging development of computational gene function prediction methods, which are targeted to analyze large scale data, and also those which use such omics data as additional source of function prediction. In this book, we overview this emerging exciting field. The authors have been selected from 1) those who develop novel purely computational methods 2) those who develop function prediction methods which use omics data 3) those who maintain and update data base of function annotation of particular model organisms (E. coli), which are frequently referred

Computational Prediction of Protein Complexes from Protein Interaction Networks

Computational Prediction of Protein Complexes from Protein Interaction Networks
A Book

by Sriganesh Srihari,Chern Han Yong,Limsoon Wong

  • Publisher : Morgan & Claypool
  • Release : 2017-05-30
  • Pages : 295
  • ISBN : 1970001534
  • Language : En, Es, Fr & De
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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.

Biological Data Mining in Protein Interaction Networks

Biological Data Mining in Protein Interaction Networks
A Book

by Li, Xiao-Li,Ng, See-Kiong

  • Publisher : IGI Global
  • Release : 2009-05-31
  • Pages : 450
  • ISBN : 1605663999
  • Language : En, Es, Fr & De
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"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-protein Interactions and Networks

Protein-protein Interactions and Networks
Identification, Computer Analysis, and Prediction

by Anna Panchenko,Teresa M. Przytycka

  • Publisher : Springer Science & Business Media
  • Release : 2010-04-06
  • Pages : 212
  • ISBN : 9781848001251
  • Language : En, Es, Fr & De
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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-Protein Interaction Networks

Protein-Protein Interaction Networks
Methods and Protocols

by Stefan Canzar,Francisca Rojas Ringeling

  • Publisher : Humana
  • Release : 2020-10-18
  • Pages : 286
  • ISBN : 9781493998753
  • Language : En, Es, Fr & De
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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.

Computational Protein-Protein Interactions

Computational Protein-Protein Interactions
A Book

by Ruth Nussinov,Gideon Schreiber

  • Publisher : CRC Press
  • Release : 2009-06-26
  • Pages : 344
  • ISBN : 9781420070071
  • Language : En, Es, Fr & De
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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 research directions, Computational Protein-Protein Interactions examines topics in the prediction of protein-protein interactions, including interference with protein-protein interactions and their design. Explores Computational Approaches to Understanding Protein-Protein Interactions Outlining fundamental and applied aspects of the usefulness of computations when approaching protein-protein interactions, this book incorporates different views of the same biochemical problem from sequence to structure to energetics. It covers protein-protein interaction prediction and dynamics, design, drug design for inhibition, and uses for the prediction of function. The text provides general chapters that overview the topic and also includes advanced material. The chapters detail the complexity of protein interaction studies and discuss potential caveats. Addresses the Next Big Problem in Molecular Biology While it is important to predict protein associations, this is a daunting task. Edited by two experts in the field and containing contributions from those at the forefront of research, the book provides a basic outline of major directions in computational protein-protein interactions research at the heart of functional genomics and crucial for drug discovery. It addresses the next big problem in molecular biology: how to create links between all the pieces of the cell jigsaw puzzle.

Protein Interaction Networks in Health and Disease

Protein Interaction Networks in Health and Disease

by Spyros Petrakis,Miguel A. Andrade-Navarro

  • Publisher : Frontiers Media SA
  • Release : 2016-10-19
  • Pages : 329
  • ISBN : 2889199827
  • Language : En, Es, Fr & De
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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.

Neuroproteomics

Neuroproteomics
A Book

by Oscar Alzate

  • Publisher : CRC Press
  • Release : 2009-10-26
  • Pages : 354
  • ISBN : 9781420076264
  • Language : En, Es, Fr & De
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In this, the post-genomic age, our knowledge of biological systems continues to expand and progress. As the research becomes more focused, so too does the data. Genomic research progresses to proteomics and brings us to a deeper understanding of the behavior and function of protein clusters. And now proteomics gives way to neuroproteomics as we begin to unravel the complex mysteries of neurological diseases that less than a generation ago seemed opaque to our inquiries, if not altogether intractable. Edited by Dr. Oscar Alzate, Neuroproteomics is the newest volume in the CRC Press Frontiers of Neuroscience Series. With an extensive background in mathematics and physics, Dr. Alzate exemplifies the newest generation of biological systems researchers. He organizes research and data contributed from all across the world to present an overview of neuroproteomics that is practical and progressive. Bolstered by each new discovery, researchers employing multiple methods of inquiry gain a deeper understanding of the key biological problems related to brain function, brain structure, and the complexity of the nervous system. This in turn is leading to new understanding about diseases of neurological deficit such as Parkinson’s and Alzheimer’s. Approaches discussed in the book include mass spectrometry, electrophoresis, chromatography, surface plasmon resonance, protein arrays, immunoblotting, computational proteomics, and molecular imaging. Writing about their own work, leading researchers detail the principles, approaches, and difficulties of the various techniques, demonstrating the questions that neuroproteomics can answer and those it raises. New challenges wait, not the least of which is the identification of potential methods to regulate the structures and functions of key protein interaction networks. Ultimately, those building on the foundation presented here will advance our understanding of the brain and show us ways to abate the suffering caused by neurological and mental diseases.

Advances in Biotechnology Research and Application: 2012 Edition

Advances in Biotechnology Research and Application: 2012 Edition
A Book

by Anonim

  • Publisher : ScholarlyEditions
  • Release : 2012-12-26
  • Pages : 1347
  • ISBN : 1464990832
  • Language : En, Es, Fr & De
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Advances in Biotechnology Research and Application / 2012 Edition is a ScholarlyEditions™ eBook that delivers timely, authoritative, and comprehensive information about Biotechnology. The editors have built Advances in Biotechnology Research and Application / 2012 Edition on the vast information databases of ScholarlyNews.™ You can expect the information about Biotechnology in this eBook to be deeper than what you can access anywhere else, as well as consistently reliable, authoritative, informed, and relevant. The content of Advances in Biotechnology Research and Application / 2012 Edition has been produced by the world’s leading scientists, engineers, analysts, research institutions, and companies. All of the content is from peer-reviewed sources, and all of it is written, assembled, and edited by the editors at ScholarlyEditions™ and available exclusively from us. You now have a source you can cite with authority, confidence, and credibility. More information is available at http://www.ScholarlyEditions.com/.

Neural Nets WIRN10

Neural Nets WIRN10
Proceedings of the 20th Italian Workshop on Neural Nets

by Bruno Apolloni,S. Bassis,Anna Esposito,Carlo Francesco Morabito

  • Publisher : IOS Press
  • Release : 2011
  • Pages : 338
  • ISBN : 1607506912
  • Language : En, Es, Fr & De
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Prediction of Protein Structures, Functions, and Interactions

Prediction of Protein Structures, Functions, and Interactions
A Book

by Janusz M. Bujnicki

  • Publisher : John Wiley & Sons
  • Release : 2008-12-23
  • Pages : 302
  • ISBN : 9780470741900
  • Language : En, Es, Fr & De
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The growing flood of new experimental data generated by genome sequencing has provided an impetus for the development of automated methods for predicting the functions of proteins that have been deduced by sequence analysis and lack experimental characterization. Prediction of Protein Structures, Functions and Interactions presents a comprehensive overview of methods for prediction of protein structure or function, with the emphasis on their availability and possibilities for their combined use. Methods of modeling of individual proteins, prediction of their interactions, and docking of complexes are put in the context of predicting gene ontology (biological process, molecular function, and cellular component) and discussed in the light of their contribution to the emerging field of systems biology. Topics covered include: first steps of protein sequence analysis and structure prediction automated prediction of protein function from sequence template-based prediction of three-dimensional protein structures: fold-recognition and comparative modelling template-free prediction of three-dimensional protein structures quality assessment of protein models prediction of molecular interactions: from small ligands to large protein complexes macromolecular docking integrating prediction of structure, function, and interactions Prediction of Protein Structures, Functions and Interactions focuses on the methods that have performed well in CASPs, and which are constantly developed and maintained, and are freely available to academic researchers either as web servers or programs for local installation. It is an essential guide to the newest, best methods for prediction of protein structure and functions, for researchers and advanced students working in structural bioinformatics, protein chemistry, structural biology and drug discovery.

Algorithmic and Artificial Intelligence Methods for Protein Bioinformatics

Algorithmic and Artificial Intelligence Methods for Protein Bioinformatics
A Book

by Yi Pan,Jianxin Wang,Min Li

  • Publisher : John Wiley & Sons
  • Release : 2013-10-07
  • Pages : 536
  • ISBN : 1118567811
  • Language : En, Es, Fr & De
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An in-depth look at the latest research, methods, and applications in the field of protein bioinformatics This book presents the latest developments in protein bioinformatics, introducing for the first time cutting-edge research results alongside novel algorithmic and AI methods for the analysis of protein data. In one complete, self-contained volume, Algorithmic and Artificial Intelligence Methods for Protein Bioinformatics addresses key challenges facing both computer scientists and biologists, arming readers with tools and techniques for analyzing and interpreting protein data and solving a variety of biological problems. Featuring a collection of authoritative articles by leaders in the field, this work focuses on the analysis of protein sequences, structures, and interaction networks using both traditional algorithms and AI methods. It also examines, in great detail, data preparation, simulation, experiments, evaluation methods, and applications. Algorithmic and Artificial Intelligence Methods for Protein Bioinformatics: Highlights protein analysis applications such as protein-related drug activity comparison Incorporates salient case studies illustrating how to apply the methods outlined in the book Tackles the complex relationship between proteins from a systems biology point of view Relates the topic to other emerging technologies such as data mining and visualization Includes many tables and illustrations demonstrating concepts and performance figures Algorithmic and Artificial Intelligence Methods for Protein Bioinformatics is an essential reference for bioinformatics specialists in research and industry, and for anyone wishing to better understand the rich field of protein bioinformatics.

Genome Research

Genome Research
A Book

by Anonim

  • Publisher : Unknown Publisher
  • Release : 2008
  • Pages : 329
  • ISBN : 9876543210XXX
  • Language : En, Es, Fr & De
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Swarm, Evolutionary, and Memetic Computing

Swarm, Evolutionary, and Memetic Computing
4th International Conference, SEMCCO 2013, Chennai, India, December 19-21, 2013, Proceedings

by Bijaya Ketan Panigrahi,Ponnuthurai Nagaratnam Suganthan,Swagatam Das,Shubhransu Sekhar Dash

  • Publisher : Springer
  • Release : 2013-12-12
  • Pages : 672
  • ISBN : 3319037560
  • Language : En, Es, Fr & De
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The two-volume set LNCS 8297 and LNCS 8298 constitutes the proceedings of the 4th International Conference on Swarm, Evolutionary and Memetic Computing, SEMCCO 2013, held in Chennai, India, in December 2013. The total of 123 papers presented in this volume was carefully reviewed and selected for inclusion in the proceedings. They cover cutting-edge research on swarm, evolutionary and memetic computing, neural and fuzzy computing and its application.

Research in Computational Molecular Biology

Research in Computational Molecular Biology
12th Annual International Conference, RECOMB 2008, Singapore, March 30 - April 2, 2008, Proceedings

by Martin Vingron,Limsoon Wong

  • Publisher : Springer
  • Release : 2008-04-03
  • Pages : 480
  • ISBN : 3540788395
  • Language : En, Es, Fr & De
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This book constitutes the refereed proceedings of the 12th Annual International Conference on Research in Computational Molecular Biology, RECOMB 2008. It presents current issues in algorithmic, theoretical, and experimental bioinformatics.

Protein Bioinformatics

Protein Bioinformatics
From Sequence to Function

by M. Michael Gromiha

  • Publisher : Academic Press
  • Release : 2011-04-21
  • Pages : 339
  • ISBN : 0123884241
  • Language : En, Es, Fr & De
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One of the most pressing tasks in biotechnology today is to unlock the function of each of the thousands of new genes identified every day. Scientists do this by analyzing and interpreting proteins, which are considered the task force of a gene. This single source reference covers all aspects of proteins, explaining fundamentals, synthesizing the latest literature, and demonstrating the most important bioinformatics tools available today for protein analysis, interpretation and prediction. Students and researchers of biotechnology, bioinformatics, proteomics, protein engineering, biophysics, computational biology, molecular modeling, and drug design will find this a ready reference for staying current and productive in this fast evolving interdisciplinary field. Explains all aspects of proteins including sequence and structure analysis, prediction of protein structures, protein folding, protein stability, and protein interactions Presents a cohesive and accessible overview of the field, using illustrations to explain key concepts and detailed exercises for students.

Of Urfs And Orfs

Of Urfs And Orfs
A Primer on How to Analyze Derived Amino Acid Sequences

by Russell F. Doolittle

  • Publisher : University Science Books
  • Release : 1986
  • Pages : 103
  • ISBN : 9780935702545
  • Language : En, Es, Fr & De
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In these days of facile cloning and rapid DNA sequencing, it is not uncommon for investigators to find themselves with a DNA sequence that may or may not code for a known gene product. The sequence is 'open' when read in an appropriate frame, which is to say that there is a long run of amino acid codons before the appearance of a terminator codon. How can we find out if this 'unidentified reading frame' (URF) really codes for a genuine protein, and how can we identify it if it exists? There are two general strategies, both of which can also be applied to the characterization of any 'open reading frame' (ORF), whether or not it has been 'identified'. The first and simplest approach involves computer searching and analysis; the second employs antibodies raised against synthetic peptides patterned on the sequence of the expected gene product. Both methods have been used with great success by many investigators. Each has, nonetheless, its pitfalls and frustrations. This primer is meant to guide the researcher past those obstacles as much as possible. Graduate students and researchers interested in amino acid sequencing; molecular biologists, biochemists, chemists, and biotechnologists.

Intelligent Computing in Bioinformatics

Intelligent Computing in Bioinformatics
10th International Conference, ICIC 2014, Taiyuan, China, August 3-6, 2014, Proceedings

by De-Shuang Huang,Kyungsook Han,Michael Gromiha

  • Publisher : Springer
  • Release : 2014-07-03
  • Pages : 510
  • ISBN : 3319093304
  • Language : En, Es, Fr & De
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This book – in conjunction with the volumes LNCS 8588 and LNAI 8589 – constitutes the refereed proceedings of the 10th International Conference on Intelligent Computing, ICIC 2014, held in Taiyuan, China, in August 2014. The 58 papers of this volume were carefully reviewed and selected from numerous submissions. The papers are organized in topical sections such as machine learning; neural networks; image processing; computational systems biology and medical informatics; biomedical informatics theory and methods; advances on bio-inspired computing; protein and gene bioinformatics: analysis, algorithms, applications.