Protein Function Prediction For Omics Era

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Protein Function Prediction for Omics Era

Author : Daisuke Kihara
Publisher : Springer Science & Business Media
ISBN 13 : 9400708815
Total Pages : 316 pages
Book Rating : 4.4/5 (7 download)

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Book Synopsis Protein Function Prediction for Omics Era by : Daisuke Kihara

Download or read book Protein Function Prediction for Omics Era written by Daisuke Kihara and published by Springer Science & Business Media. This book was released on 2011-04-19 with total page 316 pages. Available in PDF, EPUB and Kindle. Book 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

New Approaches of Protein Function Prediction from Protein Interaction Networks

Author : Jingyu Hou
Publisher : Academic Press
ISBN 13 : 0128099445
Total Pages : 124 pages
Book Rating : 4.1/5 (28 download)

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Book Synopsis New Approaches of Protein Function Prediction from Protein Interaction Networks by : Jingyu Hou

Download or read book New Approaches of Protein Function Prediction from Protein Interaction Networks written by Jingyu Hou and published by Academic Press. This book was released on 2017-01-13 with total page 124 pages. Available in PDF, EPUB and Kindle. Book 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 Function Prediction: Methods and Protocols

Author : Daisuke Kihara
Publisher : Methods in Molecular Biology
ISBN 13 : 9781493983681
Total Pages : 252 pages
Book Rating : 4.9/5 (836 download)

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Book Synopsis Protein Function Prediction: Methods and Protocols by : Daisuke Kihara

Download or read book Protein Function Prediction: Methods and Protocols written by Daisuke Kihara and published by Methods in Molecular Biology. This book was released on 2019-05-12 with total page 252 pages. Available in PDF, EPUB and Kindle. Book excerpt:

From Protein Structure to Function with Bioinformatics

Author : Daniel John Rigden
Publisher : Springer Science & Business Media
ISBN 13 : 1402090587
Total Pages : 330 pages
Book Rating : 4.4/5 (2 download)

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Book Synopsis From Protein Structure to Function with Bioinformatics by : Daniel John Rigden

Download or read book From Protein Structure to Function with Bioinformatics written by Daniel John Rigden and published by Springer Science & Business Media. This book was released on 2008-12-11 with total page 330 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Analyzing Network Data in Biology and Medicine

Author : Nataša Pržulj
Publisher : Cambridge University Press
ISBN 13 : 1108432239
Total Pages : 647 pages
Book Rating : 4.1/5 (84 download)

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Book Synopsis Analyzing Network Data in Biology and Medicine by : Nataša Pržulj

Download or read book Analyzing Network Data in Biology and Medicine written by Nataša Pržulj and published by Cambridge University Press. This book was released on 2019-03-28 with total page 647 pages. Available in PDF, EPUB and Kindle. Book excerpt: Introduces biological concepts and biotechnologies producing the data, graph and network theory, cluster analysis and machine learning, using real-world biological and medical examples.

Biological Knowledge Discovery Handbook

Author : Mourad Elloumi
Publisher : John Wiley & Sons
ISBN 13 : 1118853725
Total Pages : 1192 pages
Book Rating : 4.1/5 (188 download)

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Book Synopsis Biological Knowledge Discovery Handbook by : Mourad Elloumi

Download or read book Biological Knowledge Discovery Handbook written by Mourad Elloumi and published by John Wiley & Sons. This book was released on 2015-02-04 with total page 1192 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Protein Structure Prediction

Author : Igor F. Tsigelny
Publisher : Internat'l University Line
ISBN 13 : 9780963681775
Total Pages : 540 pages
Book Rating : 4.6/5 (817 download)

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Book Synopsis Protein Structure Prediction by : Igor F. Tsigelny

Download or read book Protein Structure Prediction written by Igor F. Tsigelny and published by Internat'l University Line. This book was released on 2002 with total page 540 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Structure-Based Drug Design for Diagnosis and Treatment of Neurological Diseases

Author : Rona R. Ramsay
Publisher : Frontiers Media SA
ISBN 13 : 2889451232
Total Pages : 206 pages
Book Rating : 4.8/5 (894 download)

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Book Synopsis Structure-Based Drug Design for Diagnosis and Treatment of Neurological Diseases by : Rona R. Ramsay

Download or read book Structure-Based Drug Design for Diagnosis and Treatment of Neurological Diseases written by Rona R. Ramsay and published by Frontiers Media SA. This book was released on 2017-03-24 with total page 206 pages. Available in PDF, EPUB and Kindle. Book excerpt: European Cooperation in Science and Technology (COST) supports the collaboration of nationally-funded science and technology research through the creation of networks. COST is the longest-running European framework enhancing cooperation among researchers, engineers and scholars across Europe. The COST Action CM1103 “Structure-based drug design for diagnosis and treatment of neurological diseases: dissecting and modulating complex function in the monoaminergic systems of the brain” is a good example of the advances possible through interdisciplinary collaboration on difficult problems. COST Action CM1103 brought together 28 research groups from 18 countries to collaborate for four years on multi-target drug design for complex neuropathologies. The interdisciplinary expertise of the members is spans the range from computational enzymology to human studies, providing outstanding opportunities for the interdisciplinary development of trainees, and is reflected in the articles in this e-book. This Research Topic covers progress in multi-target drug design for the complex neuropathologies of the monoamine system that are apparent, for example, in Alzheimer’s disease. After a mini-review to introduce the topic of multi-target drug design, the other articles review the Research topic from their own perspective, two from computational approaches, three from medicinal chemistry, two from molecular pharmacology, and two from studies in whole brain. This multi-faceted approach describes new compounds, new methodology, and advances in the basic science of understanding the brain. This Ebook is based upon work from COST Action (CM1103 “Structure-based drug design for diagnosis and treatment of neurological diseases: dissecting and modulating complex function in the monoaminergic systems of the brain"), supported by COST (European Cooperation in Science and Technology). COST (European Cooperation in Science and Technology) is a pan-European intergovernmental framework. Its mission is to enable break-through scientific and technological developments leading to new concepts and products and thereby contribute to strengthening Europe’s research and innovation capacities. It allows researchers, engineers and scholars to jointly develop their own ideas and take new initiatives across all fields of science and technology, while promoting multi- and interdisciplinary approaches. COST aims at fostering a better integration of less research intensive countries to the knowledge hubs of the European Research Area. The COST Association, an International not-for-profit Association under Belgian Law, integrates all management, governing and administrative functions necessary for the operation of the framework. The COST Association has currently 36 Member Countries. www.cost.eu

Protein Structure Prediction

Author : David Webster
Publisher : Springer Science & Business Media
ISBN 13 : 1592593682
Total Pages : 425 pages
Book Rating : 4.5/5 (925 download)

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Book Synopsis Protein Structure Prediction by : David Webster

Download or read book Protein Structure Prediction written by David Webster and published by Springer Science & Business Media. This book was released on 2008-02-03 with total page 425 pages. Available in PDF, EPUB and Kindle. Book 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.

Introduction to Protein Structure Prediction

Author : Huzefa Rangwala
Publisher : John Wiley & Sons
ISBN 13 : 111809946X
Total Pages : 611 pages
Book Rating : 4.1/5 (18 download)

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Book Synopsis Introduction to Protein Structure Prediction by : Huzefa Rangwala

Download or read book Introduction to Protein Structure Prediction written by Huzefa Rangwala and published by John Wiley & Sons. This book was released on 2011-03-16 with total page 611 pages. Available in PDF, EPUB and Kindle. Book excerpt: A look at the methods and algorithms used to predict protein structure A thorough knowledge of the function and structure of proteins is critical for the advancement of biology and the life sciences as well as the development of better drugs, higher-yield crops, and even synthetic bio-fuels. To that end, this reference sheds light on the methods used for protein structure prediction and reveals the key applications of modeled structures. This indispensable book covers the applications of modeled protein structures and unravels the relationship between pure sequence information and three-dimensional structure, which continues to be one of the greatest challenges in molecular biology. With this resource, readers will find an all-encompassing examination of the problems, methods, tools, servers, databases, and applications of protein structure prediction and they will acquire unique insight into the future applications of the modeled protein structures. The book begins with a thorough introduction to the protein structure prediction problem and is divided into four themes: a background on structure prediction, the prediction of structural elements, tertiary structure prediction, and functional insights. Within those four sections, the following topics are covered: Databases and resources that are commonly used for protein structure prediction The structure prediction flagship assessment (CASP) and the protein structure initiative (PSI) Definitions of recurring substructures and the computational approaches used for solving sequence problems Difficulties with contact map prediction and how sophisticated machine learning methods can solve those problems Structure prediction methods that rely on homology modeling, threading, and fragment assembly Hybrid methods that achieve high-resolution protein structures Parts of the protein structure that may be conserved and used to interact with other biomolecules How the loop prediction problem can be used for refinement of the modeled structures The computational model that detects the differences between protein structure and its modeled mutant Whether working in the field of bioinformatics or molecular biology research or taking courses in protein modeling, readers will find the content in this book invaluable.

Evolution of Translational Omics

Author : Institute of Medicine
Publisher : National Academies Press
ISBN 13 : 0309224187
Total Pages : 354 pages
Book Rating : 4.3/5 (92 download)

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Book Synopsis Evolution of Translational Omics by : Institute of Medicine

Download or read book Evolution of Translational Omics written by Institute of Medicine and published by National Academies Press. This book was released on 2012-09-13 with total page 354 pages. Available in PDF, EPUB and Kindle. Book excerpt: Technologies collectively called omics enable simultaneous measurement of an enormous number of biomolecules; for example, genomics investigates thousands of DNA sequences, and proteomics examines large numbers of proteins. Scientists are using these technologies to develop innovative tests to detect disease and to predict a patient's likelihood of responding to specific drugs. Following a recent case involving premature use of omics-based tests in cancer clinical trials at Duke University, the NCI requested that the IOM establish a committee to recommend ways to strengthen omics-based test development and evaluation. This report identifies best practices to enhance development, evaluation, and translation of omics-based tests while simultaneously reinforcing steps to ensure that these tests are appropriately assessed for scientific validity before they are used to guide patient treatment in clinical trials.

Plant-Derived Anticancer Drugs in the OMICS Era

Author : Deepu Pandita
Publisher : CRC Press
ISBN 13 : 1000852172
Total Pages : 323 pages
Book Rating : 4.0/5 (8 download)

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Book Synopsis Plant-Derived Anticancer Drugs in the OMICS Era by : Deepu Pandita

Download or read book Plant-Derived Anticancer Drugs in the OMICS Era written by Deepu Pandita and published by CRC Press. This book was released on 2023-10-27 with total page 323 pages. Available in PDF, EPUB and Kindle. Book excerpt: The current anti-cancer synthetic medicines are deemed inefficient and unsafe, state the editors of this new book. Plant-based lead molecules, however, such as taxol, camptothecin, podophyllotoxins, vinblastine, vincristine, homoharringtonine, and numerous other anticancer compounds from nature’s arsenal, are potentially safe and can be powerful alternatives that effectively fight against cancer. The volume looks at a variety of medicinal plants and approaches that have shown beneficial results against cancer. Topics in the book include Unani approaches of anticancer plants, genetic engineering and CRISPR/CAS-mediated editing to enhance a plant’s anticancer potential, computational approaches used in anticancer plants, and more. The volume also examines the metabolomics of plants that give them anti-cancer properties.

The Extracellular Matrix: an Overview

Author : Robert Mecham
Publisher : Springer Science & Business Media
ISBN 13 : 3642165559
Total Pages : 429 pages
Book Rating : 4.6/5 (421 download)

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Book Synopsis The Extracellular Matrix: an Overview by : Robert Mecham

Download or read book The Extracellular Matrix: an Overview written by Robert Mecham and published by Springer Science & Business Media. This book was released on 2011-02-16 with total page 429 pages. Available in PDF, EPUB and Kindle. Book excerpt: Knowledge of the extracellular matrix (ECM) is essential to understand cellular differentiation, tissue development, and tissue remodeling. This volume of the series “Biology of Extracellular Matrix” provides a timely overview of the structure, regulation, and function of the major macromolecules that make up the extracellular matrix. It covers topics such as collagen types and assembly of collagen-containing suprastructures, basement membrane, fibronectin and other cell-adhesive glycoproteins, proteoglycans, microfibrils, elastin, fibulins and matricellular proteins, such as thrombospondin. It also explores the concept that ECM components together with their cell surface receptors can be viewed as intricate nano-devices that allow cells to physically organize their 3-D-environment. Further, the role of the ECM in human disease and pathogenesis is discussed as well as the use of model organisms in elucidating ECM function.

Proteomics

Author : Stephen R. Pennington
Publisher : Springer
ISBN 13 :
Total Pages : 344 pages
Book Rating : 4.3/5 (91 download)

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Book Synopsis Proteomics by : Stephen R. Pennington

Download or read book Proteomics written by Stephen R. Pennington and published by Springer. This book was released on 2001 with total page 344 pages. Available in PDF, EPUB and Kindle. Book excerpt: Proteomics: From Protein Sequence to Function comprehensively reviews the exciting and emerging field of proteomics, the study of the protein products of the human genome. This book covers the current advances in genomics, describes existing methods for proteome analysis, and highlights the need for novel methods and instrumentation. It also presents the mechanisms of proteome data and the key applications of proteome analysis to areas such as drug discovery and cancer.

Bioactive Peptides from Food

Author : Leo M.L. Nollet
Publisher : CRC Press
ISBN 13 : 1000551938
Total Pages : 552 pages
Book Rating : 4.0/5 (5 download)

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Book Synopsis Bioactive Peptides from Food by : Leo M.L. Nollet

Download or read book Bioactive Peptides from Food written by Leo M.L. Nollet and published by CRC Press. This book was released on 2022-03-29 with total page 552 pages. Available in PDF, EPUB and Kindle. Book excerpt: A growing body of scientific evidence has revealed that many food peptides exhibit specific biological activities in addition to their established nutritional value. Bioactive peptides present in foods may help reduce the worldwide epidemic of chronic diseases that account for a great number of premature deaths annually. Bioactive peptides can be defined as isolated small fragments of proteins which provide some physiological health benefits. They act as potential modifiers reducing the risk of many chronic diseases. Bioactive Peptides from Food: Sources, Analysis, and Functions considers fundamental concepts, sources, hydrolysis, fractionation, purification, analysis, chemical synthesis, functions, and regulatory status of nutraceutical bioactive peptides. Methods of isolation of these peptides from different protein sources with their in vitro and vivo physiological effects are addressed. Divided into seven sections, this book delves into how these peptides play a major role in the development of various functional foods. Numerous bioactive peptides have been reported in recent years as naturally present or generated from food proteins of different origins like milk, eggs, soya, fish, and meat. Key Features: Includes a detailed study of the different sources of bioactive peptides Discusses the health benefits, such as antimicrobial, antiallergic, antihypertensive, antitumor, and immunomodulatory properties of peptides Explorates the state of the art analysis methods of peptides Discovers the bioinformatics of possible bioactive peptides Written by experts in their field from around the world, Bioactive Peptides from Food reveals the world of databases of peptides. It is a great resource for food scientists, technologists, chemists, nutrition researchers, producers, and processors working in the whole food science and technology field as well as those who are interested in the development of innovative functional products.

Prediction of Protein Structures, Functions, and Interactions

Author : Janusz Bujnicki
Publisher : Wiley
ISBN 13 : 0470741902
Total Pages : 302 pages
Book Rating : 4.4/5 (77 download)

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Book Synopsis Prediction of Protein Structures, Functions, and Interactions by : Janusz Bujnicki

Download or read book Prediction of Protein Structures, Functions, and Interactions written by Janusz Bujnicki and published by Wiley. This book was released on 2008-12-23 with total page 302 pages. Available in PDF, EPUB and Kindle. Book 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.

Systems Biology of Tuberculosis

Author : Johnjoe McFadden
Publisher : Springer Science & Business Media
ISBN 13 : 1461449669
Total Pages : 238 pages
Book Rating : 4.4/5 (614 download)

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Book Synopsis Systems Biology of Tuberculosis by : Johnjoe McFadden

Download or read book Systems Biology of Tuberculosis written by Johnjoe McFadden and published by Springer Science & Business Media. This book was released on 2012-12-09 with total page 238 pages. Available in PDF, EPUB and Kindle. Book excerpt: The book starts with a general introduction into the relevance of systems biology for understanding tuberculosis. This will be followed by several chapters which describe the application of systems biology to various aspects of the study of the pathogen, Mycobacterium tuberculosis, and its interaction with the host. The book provides the reader with an account of how the new science of systems biology is providing novel insights into the ancient scourge of tuberculosis. It will also describe how systems biology can be applied to the control of tuberculosis, including the development of new treatments, vaccines and diagnostics.