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Protein Function Prediction

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Protein Function Prediction

Protein Function Prediction Book
Author : Daisuke Kihara
Publisher : Humana Press
Release : 2017-05-20
ISBN : 9781493970131
Language : En, Es, Fr & De

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Book Description :

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

New Approaches of Protein Function Prediction from Protein Interaction Networks

New Approaches of Protein Function Prediction from Protein Interaction Networks Book
Author : Jingyu Hou
Publisher : Academic Press
Release : 2017-01-13
ISBN : 0128099445
Language : En, Es, Fr & De

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Book Description :

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 Protein Structure to Function with Bioinformatics

From Protein Structure to Function with Bioinformatics Book
Author : Daniel John Rigden
Publisher : Springer Science & Business Media
Release : 2008-12-11
ISBN : 1402090587
Language : En, Es, Fr & De

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Book Description :

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.

Protein Function Prediction for Omics Era

Protein Function Prediction for Omics Era Book
Author : Daisuke Kihara
Publisher : Springer Science & Business Media
Release : 2011-04-19
ISBN : 9789400708815
Language : En, Es, Fr & De

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Book Description :

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

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 Book
Author : Jeffrey Michael Yunes
Publisher :
Release : 2018
ISBN : 9780355857832
Language : En, Es, Fr & De

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Book Description :

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 Book
Author : Daniel J. Rigden
Publisher : Springer
Release : 2017-04-06
ISBN : 9402410694
Language : En, Es, Fr & De

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Book Description :

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 Book
Author : G.D. Fasman
Publisher : Springer Science & Business Media
Release : 1989-10-31
ISBN : 9780306431319
Language : En, Es, Fr & De

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Book Description :

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.

Computational Methods for Protein Structure Prediction and Modeling

Computational Methods for Protein Structure Prediction and Modeling Book
Author : Ying Xu,Dong Xu,Jie Liang
Publisher : Springer Science & Business Media
Release : 2007-08-24
ISBN : 0387683720
Language : En, Es, Fr & De

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Book Description :

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 Book
Author : Igor F. Tsigelny
Publisher : Internat'l University Line
Release : 2002
ISBN : 9780963681775
Language : En, Es, Fr & De

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Book Description :

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

Genome Wide Prediction and Analysis of Protein Protein Functional Linkages in Bacteria Book
Author : Vijaykumar Yogesh Muley,Vishal Acharya
Publisher : Springer Science & Business Media
Release : 2012-07-28
ISBN : 1461447054
Language : En, Es, Fr & De

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Book Description :

​​ ​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.

Research in Computational Molecular Biology

Research in Computational Molecular Biology Book
Author : Benny Chor
Publisher : Springer
Release : 2012-04-13
ISBN : 3642296270
Language : En, Es, Fr & De

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Book Description :

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.

Prediction of Protein Structures Functions and Interactions

Prediction of Protein Structures  Functions  and Interactions Book
Author : Janusz M. Bujnicki
Publisher : John Wiley & Sons
Release : 2008-12-23
ISBN : 9780470741900
Language : En, Es, Fr & De

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Book Description :

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.

Computational Strategies Towards Improved Protein Function Prophecy of Xylanases from Thermomyces lanuginosus

Computational Strategies Towards Improved Protein Function Prophecy of Xylanases from Thermomyces lanuginosus Book
Author : MVK Karthik,Pratyoosh Shukla
Publisher : Springer Science & Business Media
Release : 2012-07-13
ISBN : 1461447232
Language : En, Es, Fr & De

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Book Description :

This Brief reports on the interplay of an amino-acid mutation towards substrate which could lead to enhanced effects on mutant. These effects need to be given consideration in the engineering processes of protein stability and further exploration of such learning are required to provide novel indication for selection of an enzymes. There are very few reports showing such stable, energy efficient model towards improved protein function prediction screening in-silico structure based mutagenesis of xylanases from Thermomyces lanuginosus​

Biological Data Mining in Protein Interaction Networks

Biological Data Mining in Protein Interaction Networks Book
Author : Li, Xiao-Li,Ng, See-Kiong
Publisher : IGI Global
Release : 2009-05-31
ISBN : 1605663999
Language : En, Es, Fr & De

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Book Description :

"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.

Study of the Relationship Between Mus Musculus Protein Sequences and Their Biological Functions

Study of the Relationship Between Mus Musculus Protein Sequences and Their Biological Functions Book
Author : Pawan Seth
Publisher :
Release : 2007
ISBN :
Language : En, Es, Fr & De

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Book Description :

The central challenge in post-genomic era is the characterization of biological functions of newly discovered proteins. Sequence similarity based approaches infer protein functions based upon the homology between proteins. In this thesis, we present the similarity relationship between protein sequences and functions for mouse proteome in the context of gene ontology slim. The similarity between protein sequences is computed using a novel measure based upon the local BLAST alignment scores. The similarity between protein functions is characterized using the three gene ontology categories. In the study, the ontology categories are represented using a general tree structure. Three ontology trees are constructed using the definitions provided in gene ontology slim. The mouse protein sequences are then mapped onto the trees. We present the sequence similarity distributions at different levels of GO tree. The similarities of protein sequences across gene ontology levels and traversing branches are studied. The posterior probabilities for correct predictions are calculated to study the mathematical underpinnings in evaluating the similarities between the protein sequences. Our results indicate that proteins with similar amino acid sequences have similar biological functions. Although the similarity distribution in each functional group across GO levels varies from one functional group to another, the comparison between distributions of parent and child groups reveals the strong relationship between sequence and function similarity. We conclude that sequence similarity approach can function as a key measure in the prediction of biological functions of unknown proteins. Our results suggest that the posterior probability of a correct prediction could also serve as one of the key measures for protein function prediction.

Biological Knowledge Discovery Handbook

Biological Knowledge Discovery Handbook Book
Author : Mourad Elloumi,Albert Y. Zomaya
Publisher : John Wiley & Sons
Release : 2013-12-24
ISBN : 1118617118
Language : En, Es, Fr & De

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Book Description :

The first comprehensive overview of preprocessing, mining,and postprocessing of biological data Molecular biology is undergoing exponential growth in both thevolume and complexity of biological data—and knowledgediscovery offers the capacity to automate complex search and dataanalysis tasks. This book presents a vast overview of the mostrecent developments on techniques and approaches in the field ofbiological knowledge discovery and data mining (KDD)—providingin-depth fundamental and technical field information on the mostimportant topics encountered. Written by top experts, Biological Knowledge DiscoveryHandbook: Preprocessing, Mining, and Postprocessing of BiologicalData covers the three main phases of knowledge discovery (datapreprocessing, data processing—also known as datamining—and data postprocessing) and analyzes both verificationsystems and discovery systems. BIOLOGICAL DATA PREPROCESSING Part A: Biological Data Management Part B: Biological Data Modeling Part C: Biological Feature Extraction Part D Biological Feature Selection BIOLOGICAL DATA MINING Part E: Regression Analysis of Biological Data Part F Biological Data Clustering Part G: Biological Data Classification Part H: Association Rules Learning from Biological Data Part I: Text Mining and Application to Biological Data Part J: High-Performance Computing for Biological DataMining Combining sound theory with practical applications in molecularbiology, Biological Knowledge Discovery Handbook is idealfor courses in bioinformatics and biological KDD as well as forpractitioners and professional researchers in computer science,life science, and mathematics.