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New Approaches of Protein Function Prediction from Protein Interaction Networks

New Approaches of Protein Function Prediction from Protein Interaction Networks
  • Author : Jingyu Hou
  • Publisher :Unknown
  • Release Date :2017-01-13
  • Total pages :124
  • ISBN : 9780128099445
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Summary : 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 Function Prediction

Protein Function Prediction
  • Author : Daisuke Kihara
  • Publisher :Unknown
  • Release Date :2017-05-20
  • Total pages :239
  • ISBN : 1493970135
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Summary : This volume presents established bioinformatics tools and databases for function prediction of proteins. Reflecting the diversity of this active field in bioinformatics, the chapters in this book discuss a variety of tools and resources such as sequence-, structure-, systems-, and interaction-based function prediction methods, tools for functional analysis of metagenomics data, detecting moonlighting-proteins, sub-cellular localization prediction, and pathway and comparative genomics databases. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, step-by-step instructions of how to use software and web resources, use cases, and tips on troubleshooting and avoiding known pitfalls. Thorough and cutting-edge, Protein Function Prediction: Methods and Protocols is a valuable and practical guide for using bioinformatics tools for investigating protein function

Prediction of Protein Structures, Functions, and Interactions

Prediction of Protein Structures, Functions, and Interactions
  • Author : Janusz M. Bujnicki
  • Publisher :Unknown
  • Release Date :2008-12-23
  • Total pages :302
  • ISBN : 0470741902
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Summary : 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.

Protein Function Prediction for Omics Era

Protein Function Prediction for Omics Era
  • Author : Daisuke Kihara
  • Publisher :Unknown
  • Release Date :2011-04-19
  • Total pages :310
  • ISBN : 9400708815
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Summary : 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

From Protein Structure to Function with Bioinformatics

From Protein Structure to Function with Bioinformatics
  • Author : Daniel John Rigden
  • Publisher :Unknown
  • Release Date :2008-12-11
  • Total pages :328
  • ISBN : 9781402090585
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Summary : Proteins lie at the heart of almost all biological processes and have an incredibly wide range of activities. Central to the function of all proteins is their ability to adopt, stably or sometimes transiently, structures that allow for interaction with other molecules. An understanding of the structure of a protein can therefore lead us to a much improved picture of its molecular function. This realisation has been a prime motivation of recent Structural Genomics projects, involving large-scale experimental determination of protein structures, often those of proteins about which little is known of function. These initiatives have, in turn, stimulated the massive development of novel methods for prediction of protein function from structure. Since model structures may also take advantage of new function prediction algorithms, the first part of the book deals with the various ways in which protein structures may be predicted or inferred, including specific treatment of membrane and intrinsically disordered proteins. A detailed consideration of current structure-based function prediction methodologies forms the second part of this book, which concludes with two chapters, focusing specifically on case studies, designed to illustrate the real-world application of these methods. With bang up-to-date texts from world experts, and abundant links to publicly available resources, this book will be invaluable to anyone who studies proteins and the endlessly fascinating relationship between their structure and function.

Prediction of Protein Function with a Probabilistic Model for Analysis of Sequence Similarity Networks and Genomic Context

Prediction of Protein Function with a Probabilistic Model for Analysis of Sequence Similarity Networks and Genomic Context
  • Author : Jeffrey Michael Yunes
  • Publisher :Unknown
  • Release Date :2018
  • Total pages :156
  • ISBN : 0355857839
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Summary : Effusion GCA extends Effusion by integrating the chief components necessary for automating genomic context analysis. It performs its analysis over a sequence similarity -- functional association network, with a model of protein function that includes a representation of each protein's biological process, performs simultaneous inference on multiple aspects of protein function, and only propagates functional information where it is appropriate.

From Protein Structure to Function with Bioinformatics

From Protein Structure to Function with Bioinformatics
  • Author : Daniel J. Rigden
  • Publisher :Unknown
  • Release Date :2017-04-06
  • Total pages :503
  • ISBN : 9789402410693
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Summary : This book is about protein structural bioinformatics and how it can help understand and predict protein function. It covers structure-based methods that can assign and explain protein function based on overall folds, characteristics of protein surfaces, occurrence of small 3D motifs, protein-protein interactions and on dynamic properties. Such methods help extract maximum value from new experimental structures, but can often be applied to protein models. The book also, therefore, provides comprehensive coverage of methods for predicting or inferring protein structure, covering all structural classes from globular proteins and their membrane-resident counterparts to amyloid structures and intrinsically disordered proteins. The book is split into two broad sections, the first covering methods to generate or infer protein structure, the second dealing with structure-based function annotation. Each chapter is written by world experts in the field. The first section covers methods ranging from traditional homology modelling and fold recognition to fragment-based ab initio methods, and includes a chapter, new for the second edition, on structure prediction using evolutionary covariance. Membrane proteins and intrinsically disordered proteins are each assigned chapters, while two new chapters deal with amyloid structures and means to predict modes of protein-protein interaction. The second section includes chapters covering functional diversity within protein folds and means to assign function based on surface properties and recurring motifs. Further chapters cover the key roles of protein dynamics in protein function and use of automated servers for function inference. The book concludes with two chapters covering case studies of structure prediction, based respectively on crystal structures and protein models, providing numerous examples of real-world usage of the methods mentioned previously. This book is targeted at postgraduate students and academic researchers. It is most obviously of interest to protein bioinformaticians and structural biologists, but should also serve as a guide to biologists more broadly by highlighting the insights that structural bioinformatics can provide into proteins of their interest.

Prediction of Protein Structure and the Principles of Protein Conformation

Prediction of Protein Structure and the Principles of Protein Conformation
  • Author : G.D. Fasman
  • Publisher :Unknown
  • Release Date :1989-10-31
  • Total pages :798
  • ISBN : 0306431319
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Summary : The prediction of the conformation of proteins has developed from an intellectual exercise into a serious practical endeavor that has great promise to yield new stable enzymes, products of pharmacological significance, and catalysts of great potential. With the application of predic tion gaining momentum in various fields, such as enzymology and immunology, it was deemed time that a volume be published to make available a thorough evaluation of present methods, for researchers in this field to expound fully the virtues of various algorithms, to open the field to a wider audience, and to offer the scientific public an opportunity to examine carefully its successes and failures. In this manner the practitioners of the art could better evaluate the tools and the output so that their expectations and applications could be more realistic. The editor has assembled chapters by many of the main contributors to this area and simultaneously placed their programs at three national resources so that they are readily available to those who wish to apply them to their personal interests. These algorithms, written by their originators, when utilized on pes or larger computers, can instantaneously take a primary amino acid sequence and produce a two-or three-dimensional artistic image that gives satisfaction to one's esthetic sensibilities and food for thought concerning the structure and function of proteins. It is in this spirit that this volume was envisaged.

Genome-Wide Prediction and Analysis of Protein-Protein Functional Linkages in Bacteria

Genome-Wide Prediction and Analysis of Protein-Protein Functional Linkages in Bacteria
  • Author : Vijaykumar Yogesh Muley,Vishal Acharya
  • Publisher :Unknown
  • Release Date :2012-07-28
  • Total pages :60
  • ISBN : 9781461447054
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Summary : ​​ ​Using genome sequencing, one can predict possible interactions among proteins. There are very few titles that focus on protein-protein interaction predictions in bacteria. The authors will describe these methods and further highlight its use to predict various biological pathways and complexity of the cellular response to various environmental conditions. Topics include analysis of complex genome-scale protein-protein interaction networks, effects of reference genome selection on prediction accuracy, and genome sequence templates to predict protein function.

Big Data Analytics in Genomics

Big Data Analytics in Genomics
  • Author : Ka-Chun Wong
  • Publisher :Unknown
  • Release Date :2016-10-24
  • Total pages :428
  • ISBN : 9783319412795
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Summary : This contributed volume explores the emerging intersection between big data analytics and genomics. Recent sequencing technologies have enabled high-throughput sequencing data generation for genomics resulting in several international projects which have led to massive genomic data accumulation at an unprecedented pace. To reveal novel genomic insights from this data within a reasonable time frame, traditional data analysis methods may not be sufficient or scalable, forcing the need for big data analytics to be developed for genomics. The computational methods addressed in the book are intended to tackle crucial biological questions using big data, and are appropriate for either newcomers or veterans in the field.This volume offers thirteen peer-reviewed contributions, written by international leading experts from different regions, representing Argentina, Brazil, China, France, Germany, Hong Kong, India, Japan, Spain, and the USA. In particular, the book surveys three main areas: statistical analytics, computational analytics, and cancer genome analytics. Sample topics covered include: statistical methods for integrative analysis of genomic data, computation methods for protein function prediction, and perspectives on machine learning techniques in big data mining of cancer. Self-contained and suitable for graduate students, this book is also designed for bioinformaticians, computational biologists, and researchers in communities ranging from genomics, big data, molecular genetics, data mining, biostatistics, biomedical science, cancer research, medical research, and biology to machine learning and computer science. Readers will find this volume to be an essential read for appreciating the role of big data in genomics, making this an invaluable resource for stimulating further research on the topic.

Introduction to Protein Structure Prediction

Introduction to Protein Structure Prediction
  • Author : Huzefa Rangwala,George Karypis
  • Publisher :Unknown
  • Release Date :2011-03-16
  • Total pages :520
  • ISBN : 111809946X
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Summary : A look at the methods and algorithms used to predict proteinstructure A thorough knowledge of the function and structure of proteinsis critical for the advancement of biology and the life sciences aswell as the development of better drugs, higher-yield crops, andeven synthetic bio-fuels. To that end, this reference sheds lighton the methods used for protein structure prediction and revealsthe key applications of modeled structures. This indispensable bookcovers the applications of modeled protein structures and unravelsthe relationship between pure sequence information andthree-dimensional structure, which continues to be one of thegreatest challenges in molecular biology. With this resource, readers will find an all-encompassingexamination of the problems, methods, tools, servers, databases,and applications of protein structure prediction and they willacquire unique insight into the future applications of the modeledprotein structures. The book begins with a thorough introduction tothe protein structure prediction problem and is divided into fourthemes: a background on structure prediction, the prediction ofstructural elements, tertiary structure prediction, and functionalinsights. Within those four sections, the following topics arecovered: Databases and resources that are commonly used for proteinstructure prediction The structure prediction flagship assessment (CASP) and theprotein structure initiative (PSI) Definitions of recurring substructures and the computationalapproaches used for solving sequence problems Difficulties with contact map prediction and how sophisticatedmachine learning methods can solve those problems Structure prediction methods that rely on homology modeling,threading, and fragment assembly Hybrid methods that achieve high-resolution proteinstructures Parts of the protein structure that may be conserved and usedto interact with other biomolecules How the loop prediction problem can be used for refinement ofthe modeled structures The computational model that detects the differences betweenprotein structure and its modeled mutant Whether working in the field of bioinformatics or molecularbiology research or taking courses in protein modeling, readerswill find the content in this book invaluable.

Computational Methods for Protein Structure Prediction and Modeling

Computational Methods for Protein Structure Prediction and Modeling
  • Author : Ying Xu,Dong Xu,Jie Liang
  • Publisher :Unknown
  • Release Date :2007-08-24
  • Total pages :396
  • ISBN : 9780387683720
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Summary : Volume One of this two-volume sequence focuses on the basic characterization of known protein structures, and structure prediction from protein sequence information. Eleven chapters survey of the field, covering key topics in modeling, force fields, classification, computational methods, and structure prediction. Each chapter is a self contained review covering definition of the problem and historical perspective; mathematical formulation; computational methods and algorithms; performance results; existing software; strengths, pitfalls, challenges, and future research.

Protein Structure Prediction

Protein Structure Prediction
  • Author : Anna Tramontano
  • Publisher :Unknown
  • Release Date :2006-02-20
  • Total pages :228
  • ISBN : 9783527311675
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Summary : While most textbooks on bioinformatics focus on genetic algorithms and treat protein structure prediction only superficially, this course book assumes a novel and unique focus. Adopting a didactic approach, the author explains all the current methods in terms of their reliability, limitations and user-friendliness. She provides practical examples to help first-time users become familiar with the possibilities and pitfalls of computer-based structure prediction, making this a must-have for students and researchers.

Trichomonas Vaginalis Genome Annotation Validation and Protein Function Prediction Via Proteomics and Phylogenetics

Trichomonas Vaginalis Genome Annotation Validation and Protein Function Prediction Via Proteomics and Phylogenetics
  • Author : Richard Donald Hayes
  • Publisher :Unknown
  • Release Date :2009
  • Total pages :394
  • ISBN : UCLA:L0099900334
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Summary :

Research in Computational Molecular Biology

Research in Computational Molecular Biology
  • Author : Benny Chor
  • Publisher :Unknown
  • Release Date :2012-04-13
  • Total pages :372
  • ISBN : 9783642296277
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Summary : This book constitutes the refereed proceedings of the 16th Annual International Conference on Research in Computational Molecular Biology, RECOMB 2012, held in Barcelona, Spain, in April 2012. The 31 revised full papers presented together with 5 keynote lectures were carefully reviewed and selected from 200 submissions. The papers feature current research in all areas of computational molecular biology, including: molecular sequence analysis; recognition of genes and regulatory elements; molecular evolution; protein structure; structural genomics; analysis of gene expression; biological networks; sequencing and genotyping technologies; drug design; probabilistic and combinatorial algorithms; systems biology; computational proteomics; structural and functional genomics; information systems for computational biology and imaging.

Molecular Biology of the Cell

Molecular Biology of the Cell
  • Author : Bruce Alberts
  • Publisher :Unknown
  • Release Date :2004
  • Total pages :229
  • ISBN : 0815332181
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Summary :

Machine Learning Techniques on Gene Function Prediction

Machine Learning Techniques on Gene Function Prediction
  • Author : Quan Zou,Arun Kumar Sangaiah,Dariusz Mrozek
  • Publisher :Unknown
  • Release Date :2019-12-04
  • Total pages :229
  • ISBN : 9782889632145
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Summary :

Essential Bioinformatics

Essential Bioinformatics
  • Author : Jin Xiong
  • Publisher :Unknown
  • Release Date :2006-03-13
  • Total pages :229
  • ISBN : 9781139450621
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Summary : Essential Bioinformatics is a concise yet comprehensive textbook of bioinformatics, which provides a broad introduction to the entire field. Written specifically for a life science audience, the basics of bioinformatics are explained, followed by discussions of the state-of-the-art computational tools available to solve biological research problems. All key areas of bioinformatics are covered including biological databases, sequence alignment, genes and promoter prediction, molecular phylogenetics, structural bioinformatics, genomics and proteomics. The book emphasizes how computational methods work and compares the strengths and weaknesses of different methods. This balanced yet easily accessible text will be invaluable to students who do not have sophisticated computational backgrounds. Technical details of computational algorithms are explained with a minimum use of mathematical formulae; graphical illustrations are used in their place to aid understanding. The effective synthesis of existing literature as well as in-depth and up-to-date coverage of all key topics in bioinformatics make this an ideal textbook for all bioinformatics courses taken by life science students and for researchers wishing to develop their knowledge of bioinformatics to facilitate their own research.

XIII Mediterranean Conference on Medical and Biological Engineering and Computing 2013

XIII Mediterranean Conference on Medical and Biological Engineering and Computing 2013
  • Author : Laura M. Roa Romero
  • Publisher :Unknown
  • Release Date :2013-10-01
  • Total pages :1104
  • ISBN : 9783319008462
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Summary : The general theme of MEDICON 2013 is "Research and Development of Technology for Sustainable Healthcare". This decade is being characterized by the appearance and use of emergent technologies under development. This situation has produced a tremendous impact on Medicine and Biology from which it is expected an unparalleled evolution in these disciplines towards novel concept and practices. The consequence will be a significant improvement in health care and well-fare, i.e. the shift from a reactive medicine to a preventive medicine. This shift implies that the citizen will play an important role in the healthcare delivery process, what requires a comprehensive and personalized assistance. In this context, society will meet emerging media, incorporated to all objects, capable of providing a seamless, adaptive, anticipatory, unobtrusive and pervasive assistance. The challenge will be to remove current barriers related to the lack of knowledge required to produce new opportunities for all the society, while new paradigms are created for this inclusive society to be socially and economically sustainable, and respectful with the environment. In this way, these proceedings focus on the convergence of biomedical engineering topics ranging from formalized theory through experimental science and technological development to practical clinical applications.

Protein Structure and Function Prediction

Protein Structure and Function Prediction
  • Author : Albion E. Baucom
  • Publisher :Unknown
  • Release Date :2000
  • Total pages :206
  • ISBN : UCAL:X68101
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Summary :

Biological Data Mining in Protein Interaction Networks

Biological Data Mining in Protein Interaction Networks
  • Author : Li, Xiao-Li,Ng, See-Kiong
  • Publisher :Unknown
  • Release Date :2009-05-31
  • Total pages :450
  • ISBN : 9781605663999
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Summary : "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.