Protein Function Prediction

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New Approaches of Protein Function Prediction from Protein Interaction Networks

Author : Jingyu Hou
Publisher : Academic Press
ISBN 13 : 0128099445
Total Pages : 126 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 126 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

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.

Prediction of Protein Structures, Functions, and Interactions

Author : Janusz M. Bujnicki
Publisher : John Wiley & Sons
ISBN 13 : 9780470741900
Total Pages : 302 pages
Book Rating : 4.7/5 (419 download)

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

Download or read book Prediction of Protein Structures, Functions, and Interactions written by Janusz M. Bujnicki and published by John Wiley & Sons. 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.

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.

The Semantic Web

Author : Vipul Kashyap
Publisher : Springer Science & Business Media
ISBN 13 : 3540764526
Total Pages : 415 pages
Book Rating : 4.5/5 (47 download)

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Book Synopsis The Semantic Web by : Vipul Kashyap

Download or read book The Semantic Web written by Vipul Kashyap and published by Springer Science & Business Media. This book was released on 2008-09-27 with total page 415 pages. Available in PDF, EPUB and Kindle. Book 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

Author : G.D. Fasman
Publisher : Springer Science & Business Media
ISBN 13 : 1461315719
Total Pages : 796 pages
Book Rating : 4.4/5 (613 download)

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Book Synopsis Prediction of Protein Structure and the Principles of Protein Conformation by : G.D. Fasman

Download or read book Prediction of Protein Structure and the Principles of Protein Conformation written by G.D. Fasman and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 796 pages. Available in PDF, EPUB and Kindle. Book 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.

Molecular Biology of the Cell

Author :
Publisher :
ISBN 13 : 9780815332183
Total Pages : 0 pages
Book Rating : 4.3/5 (321 download)

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Book Synopsis Molecular Biology of the Cell by :

Download or read book Molecular Biology of the Cell written by and published by . This book was released on 2002 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Essential Bioinformatics

Author : Jin Xiong
Publisher : Cambridge University Press
ISBN 13 : 113945062X
Total Pages : 360 pages
Book Rating : 4.1/5 (394 download)

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Book Synopsis Essential Bioinformatics by : Jin Xiong

Download or read book Essential Bioinformatics written by Jin Xiong and published by Cambridge University Press. This book was released on 2006-03-13 with total page 360 pages. Available in PDF, EPUB and Kindle. Book 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 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.

Biological Sequence Analysis

Author : Richard Durbin
Publisher : Cambridge University Press
ISBN 13 : 113945739X
Total Pages : 372 pages
Book Rating : 4.1/5 (394 download)

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Book Synopsis Biological Sequence Analysis by : Richard Durbin

Download or read book Biological Sequence Analysis written by Richard Durbin and published by Cambridge University Press. This book was released on 1998-04-23 with total page 372 pages. Available in PDF, EPUB and Kindle. Book excerpt: Probabilistic models are becoming increasingly important in analysing the huge amount of data being produced by large-scale DNA-sequencing efforts such as the Human Genome Project. For example, hidden Markov models are used for analysing biological sequences, linguistic-grammar-based probabilistic models for identifying RNA secondary structure, and probabilistic evolutionary models for inferring phylogenies of sequences from different organisms. This book gives a unified, up-to-date and self-contained account, with a Bayesian slant, of such methods, and more generally to probabilistic methods of sequence analysis. Written by an interdisciplinary team of authors, it aims to be accessible to molecular biologists, computer scientists, and mathematicians with no formal knowledge of the other fields, and at the same time present the state-of-the-art in this new and highly important field.

Protein Structure Prediction

Author : Mohammed Zaki
Publisher : Springer Science & Business Media
ISBN 13 : 1588297527
Total Pages : 338 pages
Book Rating : 4.5/5 (882 download)

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Book Synopsis Protein Structure Prediction by : Mohammed Zaki

Download or read book Protein Structure Prediction written by Mohammed Zaki and published by Springer Science & Business Media. This book was released on 2007-09-12 with total page 338 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book covers elements of both the data-driven comparative modeling approach to structure prediction and also recent attempts to simulate folding using explicit or simplified models. Despite the unsolved mystery of how a protein folds, advances are being made in predicting the interactions of proteins with other molecules. Also rapidly advancing are the methods for solving the inverse folding problem, the problem of finding a sequence to fit a structure. This book focuses on the various computational methods for prediction, their successes and their limitations, from the perspective of their most well known practitioners.

Homology Molecular Modeling

Author : Rafael Trindade Maia
Publisher : BoD – Books on Demand
ISBN 13 : 1839628057
Total Pages : 147 pages
Book Rating : 4.8/5 (396 download)

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Book Synopsis Homology Molecular Modeling by : Rafael Trindade Maia

Download or read book Homology Molecular Modeling written by Rafael Trindade Maia and published by BoD – Books on Demand. This book was released on 2021-03-10 with total page 147 pages. Available in PDF, EPUB and Kindle. Book 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.

Graph Neural Networks: Foundations, Frontiers, and Applications

Author : Lingfei Wu
Publisher : Springer Nature
ISBN 13 : 9811660549
Total Pages : 701 pages
Book Rating : 4.8/5 (116 download)

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Book Synopsis Graph Neural Networks: Foundations, Frontiers, and Applications by : Lingfei Wu

Download or read book Graph Neural Networks: Foundations, Frontiers, and Applications written by Lingfei Wu and published by Springer Nature. This book was released on 2022-01-03 with total page 701 pages. Available in PDF, EPUB and Kindle. Book excerpt: Deep Learning models are at the core of artificial intelligence research today. It is well known that deep learning techniques are disruptive for Euclidean data, such as images or sequence data, and not immediately applicable to graph-structured data such as text. This gap has driven a wave of research for deep learning on graphs, including graph representation learning, graph generation, and graph classification. The new neural network architectures on graph-structured data (graph neural networks, GNNs in short) have performed remarkably on these tasks, demonstrated by applications in social networks, bioinformatics, and medical informatics. Despite these successes, GNNs still face many challenges ranging from the foundational methodologies to the theoretical understandings of the power of the graph representation learning. This book provides a comprehensive introduction of GNNs. It first discusses the goals of graph representation learning and then reviews the history, current developments, and future directions of GNNs. The second part presents and reviews fundamental methods and theories concerning GNNs while the third part describes various frontiers that are built on the GNNs. The book concludes with an overview of recent developments in a number of applications using GNNs. This book is suitable for a wide audience including undergraduate and graduate students, postdoctoral researchers, professors and lecturers, as well as industrial and government practitioners who are new to this area or who already have some basic background but want to learn more about advanced and promising techniques and applications.

Bioinformatics: Sequences, Structures, Phylogeny

Author : Asheesh Shanker
Publisher : Springer
ISBN 13 : 9811315620
Total Pages : 402 pages
Book Rating : 4.8/5 (113 download)

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Book Synopsis Bioinformatics: Sequences, Structures, Phylogeny by : Asheesh Shanker

Download or read book Bioinformatics: Sequences, Structures, Phylogeny written by Asheesh Shanker and published by Springer. This book was released on 2018-10-13 with total page 402 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book provides a comprehensive overview of the concepts and approaches used for sequence, structure, and phylogenetic analysis. Starting with an introduction to the subject and intellectual property protection for bioinformatics, it guides readers through the latest sequencing technologies, sequence analysis, genomic variations, metagenomics, epigenomics, molecular evolution and phylogenetics, structural bioinformatics, protein folding, structure analysis and validation, drug discovery, reverse vaccinology, machine learning, application of R programming in biological data analysis, and the use of Linux in handling large data files.

Sequence — Evolution — Function

Author : Eugene V. Koonin
Publisher : Springer Science & Business Media
ISBN 13 : 1475737831
Total Pages : 482 pages
Book Rating : 4.4/5 (757 download)

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Book Synopsis Sequence — Evolution — Function by : Eugene V. Koonin

Download or read book Sequence — Evolution — Function written by Eugene V. Koonin and published by Springer Science & Business Media. This book was released on 2013-06-29 with total page 482 pages. Available in PDF, EPUB and Kindle. Book excerpt: Sequence - Evolution - Function is an introduction to the computational approaches that play a critical role in the emerging new branch of biology known as functional genomics. The book provides the reader with an understanding of the principles and approaches of functional genomics and of the potential and limitations of computational and experimental approaches to genome analysis. Sequence - Evolution - Function should help bridge the "digital divide" between biologists and computer scientists, allowing biologists to better grasp the peculiarities of the emerging field of Genome Biology and to learn how to benefit from the enormous amount of sequence data available in the public databases. The book is non-technical with respect to the computer methods for genome analysis and discusses these methods from the user's viewpoint, without addressing mathematical and algorithmic details. Prior practical familiarity with the basic methods for sequence analysis is a major advantage, but a reader without such experience will be able to use the book as an introduction to these methods. This book is perfect for introductory level courses in computational methods for comparative and functional genomics.

Big Data Analytics in Genomics

Author : Ka-Chun Wong
Publisher : Springer
ISBN 13 : 3319412795
Total Pages : 426 pages
Book Rating : 4.3/5 (194 download)

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Book Synopsis Big Data Analytics in Genomics by : Ka-Chun Wong

Download or read book Big Data Analytics in Genomics written by Ka-Chun Wong and published by Springer. This book was released on 2016-10-24 with total page 426 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Prediction of Protein Secondary Structure

Author : Yaoqi Zhou
Publisher : Humana
ISBN 13 : 9781493964048
Total Pages : 0 pages
Book Rating : 4.9/5 (64 download)

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Book Synopsis Prediction of Protein Secondary Structure by : Yaoqi Zhou

Download or read book Prediction of Protein Secondary Structure written by Yaoqi Zhou and published by Humana. This book was released on 2016-10-28 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: This thorough volume explores predicting one-dimensional functional properties, functional sites in particular, from protein sequences, an area which is getting more and more attention. Beginning with secondary structure prediction based on sequence only, the book continues by exploring secondary structure prediction based on evolution information, prediction of solvent accessible surface areas and backbone torsion angles, model building, global structural properties, functional properties, as well as visualizing interior and protruding regions in proteins. Written for the highly successful Methods in Molecular Biology series, the chapters include the kind of detail and implementation advice to ensure success in the laboratory. Practical and authoritative, Prediction of Protein Secondary Structure serves as a vital guide to numerous state-of-the-art techniques that are useful for computational and experimental biologists.