New Approaches of Protein Function Prediction from Protein Interaction Networks Book

New Approaches of Protein Function Prediction from Protein Interaction Networks


  • Author : Jingyu Hou
  • Publisher : Academic Press
  • Release Date : 2017-01-13
  • Genre: Mathematics
  • Pages : 124
  • ISBN 10 : 9780128099445

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New Approaches of Protein Function Prediction from Protein Interaction Networks Excerpt :

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

Prediction of Protein Structures  Functions  and Interactions Book

Prediction of Protein Structures Functions and Interactions


  • Author : Janusz M. Bujnicki
  • Publisher : John Wiley & Sons
  • Release Date : 2008-12-23
  • Genre: Science
  • Pages : 302
  • ISBN 10 : 0470741902

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Prediction of Protein Structures Functions and Interactions Excerpt :

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.

Introduction to Protein Structure Prediction Book

Introduction to Protein Structure Prediction


  • Author : Huzefa Rangwala
  • Publisher : John Wiley & Sons
  • Release Date : 2011-03-16
  • Genre: Science
  • Pages : 520
  • ISBN 10 : 111809946X

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Introduction to Protein Structure Prediction Excerpt :

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 comput

Homology Molecular Modeling Book

Homology Molecular Modeling


  • Author : Rafael Trindade Maia
  • Publisher : BoD – Books on Demand
  • Release Date : 2021-03-10
  • Genre: Science
  • Pages : 147
  • ISBN 10 : 9781839628054

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Homology Molecular Modeling Excerpt :

Homology modeling is an extremely useful and versatile technique that is gaining more and more space and demand in research in computational and theoretical biology. This book, “Homology Molecular Modeling - Perspectives and Applications”, brings together unpublished chapters on this technique. In this book, 7 chapters are intimately related to the theme of molecular modeling, carefully selected and edited for academic and scientific readers. It is an indispensable read for anyone interested in the areas of bioinformatics and computational biology. Divided into 4 sections, the reader will have a didactic and comprehensive view of the theme, with updated and relevant concepts on the subject. This book was organized from researchers to researchers with the aim of spreading the fascinating area of molecular modeling by homology.

Bioinformatics and Human Genomics Research Book

Bioinformatics and Human Genomics Research


  • Author : Diego A. Forero
  • Publisher : CRC Press
  • Release Date : 2021-12-23
  • Genre: Science
  • Pages : 509
  • ISBN 10 : 9781000405682

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Bioinformatics and Human Genomics Research Excerpt :

Advances in high-throughput biological methods have led to the publication of a large number of genome-wide studies in human and animal models. In this context, recent tools from bioinformatics and computational biology have been fundamental for the analysis of these genomic studies. The book Bioinformatics and Human Genomics Research provides updated and comprehensive information about multiple approaches of the application of bioinformatic tools to research in human genomics. It covers strategies analysis of genome-wide association studies, genome-wide expression studies and genome-wide DNA methylation, among other topics. It provides interesting strategies for data mining in human genomics, network analysis, prediction of binding sites for miRNAs and transcription factors, among other themes. Experts from all around the world in bioinformatics and human genomics have contributed chapters in this book. Readers will find this book as quite useful for their in silico explorations, which would contribute to a better and deeper understanding of multiple biological processes and of pathophysiology of many human diseases.

New Approaches of Protein Function Prediction from Protein Interaction Networks Book

New Approaches of Protein Function Prediction from Protein Interaction Networks


  • Author : Jingyu Hou
  • Publisher : Academic Press
  • Release Date : 2017-01-15
  • Genre: Uncategoriezed
  • Pages : 124
  • ISBN 10 : 0128098147

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New Approaches of Protein Function Prediction from Protein Interaction Networks Excerpt :

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 Structure Prediction Book

Protein Structure Prediction


  • Author : David Webster
  • Publisher : Springer Science & Business Media
  • Release Date : 2008-02-03
  • Genre: Science
  • Pages : 425
  • ISBN 10 : 9781592593682

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Protein Structure Prediction Excerpt :

The number of protein sequences grows each year, yet the number of structures deposited in the Protein Data Bank remains relatively small. The importance of protein structure prediction cannot be overemphasized, and this volume is a timely addition to the literature in this field. Protein Structure Prediction: Methods and Protocols is a departure from the normal Methods in Molecular Biology series format. By its very nature, protein structure prediction demands that there be a greater mix of theoretical and practical aspects than is normally seen in this series. This book is aimed at both the novice and the experienced researcher who wish for detailed inf- mation in the field of protein structure prediction; a major intention here is to include important information that is needed in the day-to-day work of a research scientist, important information that is not always decipherable in scientific literature. Protein Structure Prediction: Methods and Protocols covers the topic of protein structure prediction in an eclectic fashion, detailing aspects of pred- tion that range from sequence analysis (a starting point for many algorithms) to secondary and tertiary methods, on into the prediction of docked complexes (an essential point in order to fully understand biological function). As this volume progresses, the authors contribute their expert knowledge of protein structure prediction to many disciplines, such as the identification of motifs and domains, the comparative modeling of proteins, and ab initio approaches to protein loop, side chain, and protein prediction.

Protein Bioinformatics Book

Protein Bioinformatics


  • Author : M. Michael Gromiha
  • Publisher : Academic Press
  • Release Date : 2011-04-21
  • Genre: Computers
  • Pages : 339
  • ISBN 10 : 9780123884244

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Protein Bioinformatics Excerpt :

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.

The Semantic Web Book
Score: 5
From 1 Ratings

The Semantic Web


  • Author : Vipul Kashyap
  • Publisher : Springer Science & Business Media
  • Release Date : 2008-08-15
  • Genre: Computers
  • Pages : 415
  • ISBN 10 : 9783540764519

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The Semantic Web Excerpt :

The Semantic Web is a vision – the idea of having data on the Web defined and linked in such a way that it can be used by machines not just for display purposes but for automation, integration and reuse of data across various applications. However, there is a widespread misconception that the Semantic Web is a rehash of existing AI and database work. Kashyap, Bussler, and Moran dispel this notion by presenting the multi-disciplinary technological underpinnings such as machine learning, information retrieval, service-oriented architectures, and grid computing. Thus they combine the informational and computational aspects needed to realize the full potential of the Semantic Web vision.

Prediction of Protein Structure and the Principles of Protein Conformation Book

Prediction of Protein Structure and the Principles of Protein Conformation


  • Author : G.D. Fasman
  • Publisher : Springer Science & Business Media
  • Release Date : 2012-12-06
  • Genre: Science
  • Pages : 798
  • ISBN 10 : 9781461315711

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Prediction of Protein Structure and the Principles of Protein Conformation Excerpt :

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.

Essential Bioinformatics Book
Score: 4.5
From 6 Ratings

Essential Bioinformatics


  • Author : Jin Xiong
  • Publisher : Cambridge University Press
  • Release Date : 2006-03-13
  • Genre: Science
  • Pages : null
  • ISBN 10 : 9781139450621

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Essential Bioinformatics Excerpt :

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.

Protein Function Prediction for Omics Era Book

Protein Function Prediction for Omics Era


  • Author : Daisuke Kihara
  • Publisher : Springer Science & Business Media
  • Release Date : 2011-04-19
  • Genre: Medical
  • Pages : 310
  • ISBN 10 : 9789400708815

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Protein Function Prediction for Omics Era Excerpt :

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

Molecular Biology of the Cell Book
Score: 4.5
From 5 Ratings

Molecular Biology of the Cell


  • Author : Bruce Alberts
  • Publisher : Unknown
  • Release Date : 2004
  • Genre: Uncategoriezed
  • Pages : null
  • ISBN 10 : 0815332181

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Molecular Biology of the Cell Excerpt :

Protein Function Prediction from Protein Interaction Network Book

Protein Function Prediction from Protein Interaction Network


  • Author : Sovan Saha
  • Publisher : LAP Lambert Academic Publishing
  • Release Date : 2013
  • Genre: Uncategoriezed
  • Pages : 148
  • ISBN 10 : 3659402788

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Protein Function Prediction from Protein Interaction Network Excerpt :

Proteins perform every function in a cell. With the advent of genome sequencing projects for different organisms, large amounts of DNA and protein sequence data is available, whereas their biological function is still unknown in the most of the cases. Predicting protein function is the most challenging problem in post-genomic era. Using sequence homology, phylogenetic profiles, gene expression data, and function of unknown protein can be predicted. Recently, the large interaction networks constructed from high throughput techniques like Yeast2Hybrid experiments are also used in prediction of protein function. As experimental techniques for detection and validation of protein interactions are time consuming, there is a need for computational methods for this task. Based on the concept that a protein performs similar function like its neighbor in protein interaction network, a method is proposed to predict protein function using protein-protein interaction data.This analysis should enlighten the path for predicting unannotated protein function hence identifying diseases and inventing methods of it's cureness.

Bioinformatics Book
Score: 3
From 1 Ratings

Bioinformatics


  • Author : Christine Orengo
  • Publisher : Taylor & Francis
  • Release Date : 2003-12-16
  • Genre: Science
  • Pages : 406
  • ISBN 10 : 9781135325237

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Bioinformatics Excerpt :

Bioinformatics, the use of computers to address biological questions, has become an essential tool in biological research. It is one of the critical keys needed to unlock the information encoded in the flood of data generated by genome, protein structure, transcriptome and proteome research. Bioinformatics: Genes, Proteins & Computers covers both the more traditional approaches to bioinformatics, including gene and protein sequence analysis and structure prediction, and more recent technologies such as datamining of transcriptomic and proteomic data to provide insights on cellular mechanisms and the causes of disease.