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.

Protein Bioinformatics Book

Protein Bioinformatics


  • Author : Cathy Wu
  • Publisher : Humana Press
  • Release Date : 2017-02-20
  • Genre: Science
  • Pages : 472
  • ISBN 10 : 1493967819

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Protein Bioinformatics Excerpt :

This volume introduces bioinformatics research methods for proteins, with special focus on protein post-translational modifications (PTMs) and networks. This book is organized into four parts and covers the basic framework and major resources for analysis of protein sequence, structure, and function; approaches and resources for analysis of protein PTMs, protein-protein interactions (PPIs) and protein networks, including tools for PPI prediction and approaches for the construction of PPI and PTM networks; and bioinformatics approaches in proteomics, including computational methods for mass spectrometry-based proteomics and integrative analysis for alternative splice isoforms, for functional discovery. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory or computational protocols, and tips on troubleshooting and avoiding known pitfalls. Cutting-edge and thorough, Protein Bioinformatics: From Protein Modifications and Networks to Proteomics is a valuable resource for readers who wish to learn about state-of-the-art bioinformatics databases and tools, novel computational methods, and future trends in protein and proteomic data analysis in systems biology. This book is useful to researchers who work in the biotechnology and pharmaceutical industries, and in various academic departments, such as biological and medical sciences and computer sciences and engineering.

The Ten Most Wanted Solutions in Protein Bioinformatics Book

The Ten Most Wanted Solutions in Protein Bioinformatics


  • Author : Anna Tramontano
  • Publisher : CRC Press
  • Release Date : 2005-05-24
  • Genre: Mathematics
  • Pages : 216
  • ISBN 10 : 9781420035001

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The Ten Most Wanted Solutions in Protein Bioinformatics Excerpt :

Utilizing high speed computational methods to extrapolate to the rest of the protein universe, the knowledge accumulated on a subset of examples, protein bioinformatics seeks to accomplish what was impossible before its invention, namely the assignment of functions or functional hypotheses for all known proteins. The Ten Most Wanted Solutions in Protein Bioinformatics considers the ten most significant problems occupying those looking to identify the biological properties and functional roles of proteins. - Problem One considers the challenge involved with detecting the existence of an evolutionary relationship between proteins. - Two and Three studies the detection of local similarities between protein sequences and analysis in order to determine functional assignment. - Four, Five, and Six look at how the knowledge of the three-dimensional structures of proteins can be experimentally determined or inferred, and then exploited to understand the role of a protein. - Seven and Eight explore how proteins interact with each other and with ligands, both physically and logically. - Nine moves us out of the realm of observation to discuss the possibility of designing completely new proteins tailored to specific tasks. - And lastly, Problem Ten considers ways to modify the functional properties of proteins. After summarizing each problem, the author looks at and evaluates the current approaches being utilized, before going on to consider some potential approaches.

From Protein Structure to Function with Bioinformatics Book

From Protein Structure to Function with Bioinformatics


  • Author : Daniel John Rigden
  • Publisher : Springer Science & Business Media
  • Release Date : 2008-12-11
  • Genre: Science
  • Pages : 328
  • ISBN 10 : 9781402090585

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From Protein Structure to Function with Bioinformatics 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.

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.

Practical Protein Bioinformatics Book

Practical Protein Bioinformatics


  • Author : Florencio Pazos
  • Publisher : Springer
  • Release Date : 2014-11-28
  • Genre: Science
  • Pages : 106
  • ISBN 10 : 9783319127279

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Practical Protein Bioinformatics Excerpt :

This book describes more than 60 web-accessible computational tools for protein analysis and is totally practical, with detailed explanations on how to use these tools and interpret their results and minimal mentions to their theoretical basis (only when that is required for making a better use of them). It covers a wide range of tools for dealing with different aspects of proteins, from their sequences, to their three-dimensional structures, and the biological networks they are immersed in. The selection of tools is based on the experience of the authors that lead a protein bioinformatics facility in a large research centre, with the additional constraint that the tools should be accessible through standard web browsers without requiring the local installation of specific software, command-line tools, etc. The web tools covered include those aimed to retrieve protein information, look for similar proteins, generate pair-wise and multiple sequence alignments of protein sequences, work with protein domains and motifs, study the phylogeny of a family of proteins, retrieve, manipulate and visualize protein three-dimensional structures, predict protein structural features as well as whole three-dimensional structures, extract biological information from protein structures, summarize large protein sets, study protein interaction and metabolic networks, etc. The book is associated to a dynamic web site that will reflect changes in the web addresses of the tools, updates of these, etc. It also contains QR codes that can be scanned with any device to direct its browser to the tool web site. This monograph will be most valuable for researchers in experimental labs without specific knowledge on bioinformatics or computing.

Structural Bioinformatics of Membrane Proteins Book

Structural Bioinformatics of Membrane Proteins


  • Author : D. Frishman
  • Publisher : Springer Science & Business Media
  • Release Date : 2011-01-22
  • Genre: Computers
  • Pages : 281
  • ISBN 10 : 9783709100455

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Structural Bioinformatics of Membrane Proteins Excerpt :

This book is the first one specifically dedicated to the structural bioinformatics of membrane proteins. With a focus on membrane proteins from the perspective of bioinformatics, the present work covers a broad spectrum of topics in evolution, structure, function, and bioinformatics of membrane proteins focusing on the most recent experimental results. Leaders in the field who have recently reported breakthrough advances cover algorithms, databases and their applications to the subject. The increasing number of recently solved membrane protein structures makes the expert coverage presented here very timely. Structural bioinformatics of membrane proteins has been an active area of research over the last thee decades and proves to be a growing field of interest.

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

Protein Bioinformatics Book

Protein Bioinformatics


  • Author : Ingvar Eidhammer
  • Publisher : Wiley-Blackwell
  • Release Date : 2004-02-13
  • Genre: Mathematics
  • Pages : 384
  • ISBN 10 : UOM:39015058724942

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Protein Bioinformatics Excerpt :

Pairwise global alignment of sequences. Pairwise local alignment and database search. Statical analysis. Multiple global alignment and phylogenetic trees. Scoring matrices. Profiles. Sequence patterns. Structures and structure descriptions. Superposition and Dynamic programming. Geometric techniques. Clustering: Combining local similarities. Significance and assessment of structure comparisons. Multiple structure comparison. Protein structure classification. Structure prediction: Threading. Basics in mathematics, probability and algorithms. Introduction to molecular biology.

Bioinformatics Book
Score: 4.5
From 3 Ratings

Bioinformatics


  • Author : Andreas D. Baxevanis
  • Publisher : John Wiley & Sons
  • Release Date : 2004-03-24
  • Genre: Computers
  • Pages : 504
  • ISBN 10 : 9780471461012

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Bioinformatics Excerpt :

"In this book, Andy Baxevanis and Francis Ouellette . . . haveundertaken the difficult task of organizing the knowledge in thisfield in a logical progression and presenting it in a digestibleform. And they have done an excellent job. This fine text will makea major impact on biological research and, in turn, on progress inbiomedicine. We are all in their debt." —Eric Lander from the Foreword Reviews from the First Edition "...provides a broad overview of the basic tools for sequenceanalysis ... For biologists approaching this subject for the firsttime, it will be a very useful handbook to keep on the shelf afterthe first reading, close to the computer." —Nature Structural Biology "...should be in the personal library of any biologist who usesthe Internet for the analysis of DNA and protein sequencedata." —Science "...a wonderful primer designed to navigate the novice throughthe intricacies of in scripto analysis ... The accomplished genesearcher will also find this book a useful addition to theirlibrary ... an excellent reference to the principles ofbioinformatics." —Trends in Biochemical Sciences This new edition of the highly successful Bioinformatics:A Practical Guide to the Analysis of Genes and Proteinsprovides a sound foundation of basic concepts, with practicaldiscussions and comparisons of both computational tools anddatabases relevant to biological research. Equipping biologists with the modern tools necessary to solvepractical problems in sequence data analysis, the Second Editioncovers the broad spectrum of topics in bioinformatics, ranging fromInternet concepts to predictive algorithms used on sequence,structure, and expression data. With chapters written by experts inthe field, this up-to-date reference thoroughly covers vitalconcepts and is appropriate for both the novice and the experiencedpractitioner. Written in clear, simple language, the book isaccessible to users without an advanced mathematical or computerscience background. This new edi

Scalable Big Data Analytics for Protein Bioinformatics Book

Scalable Big Data Analytics for Protein Bioinformatics


  • Author : Dariusz Mrozek
  • Publisher : Unknown
  • Release Date : 2018
  • Genre: Proteins
  • Pages : null
  • ISBN 10 : 3319988409

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Scalable Big Data Analytics for Protein Bioinformatics Excerpt :

This book presents a focus on proteins and their structures. The text describes various scalable solutions for protein structure similarity searching, carried out at main representation levels and for prediction of 3D structures of proteins. Emphasis is placed on techniques that can be used to accelerate similarity searches and protein structure modeling processes. The content of the book is divided into four parts. The first part provides background information on proteins and their representation levels, including a formal model of a 3D protein structure used in computational processes, and a brief overview of the technologies used in the solutions presented in the book. The second part of the book discusses Cloud services that are utilized in the development of scalable and reliable cloud applications for 3D protein structure similarity searching and protein structure prediction. The third part of the book shows the utilization of scalable Big Data computational frameworks, like Hadoop and Spark, in massive 3D protein structure alignments and identification of intrinsically disordered regions in protein structures. The fourth part of the book focuses on finding 3D protein structure similarities, accelerated with the use of GPUs and the use of multithreading and relational databases for efficient approximate searching on protein secondary structures. The book introduces advanced techniques and computational architectures that benefit from recent achievements in the field of computing and parallelism. Recent developments in computer science have allowed algorithms previously considered too time-consuming to now be efficiently used for applications in bioinformatics and the life sciences. Given its depth of coverage, the book will be of interest to researchers and software developers working in the fields of structural bioinformatics and biomedical databases.

Proteomics in Functional Genomics Book

Proteomics in Functional Genomics


  • Author : P. Jolles
  • Publisher : Birkhäuser
  • Release Date : 2013-03-11
  • Genre: Science
  • Pages : 236
  • ISBN 10 : 9783034884587

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Proteomics in Functional Genomics Excerpt :

A wealth of information has accumulated over the last few years on the human genome. The new insights have completely changed the focus of protein analysis. It is no longer time-consuming analysis of unknown products, but rather selective identifications of individual forms, modifications and processings, and overall analysis of global protein outputs from cells and tissues in health and disease. This book gears to the rising need of sensitive, accurate, and fast separation and identification techniques in proteomics. It discusses current methodologies of modern protein analysis, from isolation and sample preparation, over analysis and identification, to final characterization. Several evaluations concentrate on the now productive approaches of two-dimensional gel electrophoresis and mass spectrometry, but alternative methods and further perspectives are also outlined. The book includes an overlook over current databases to connect protein analysis data with all available information,...

Proteomics and Protein Protein Interactions Book
Score: 4
From 1 Ratings

Proteomics and Protein Protein Interactions


  • Author : Gabriel Waksman
  • Publisher : Springer Science & Business Media
  • Release Date : 2005-12-21
  • Genre: Medical
  • Pages : 348
  • ISBN 10 : 0387245316

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Proteomics and Protein Protein Interactions Excerpt :

The rapidly evolving field of protein science has now come to realize the ubiquity and importance of protein-protein interactions. It had been known for some time that proteins may interact with each other to form functional complexes, but it was thought to be the property of only a handful of key proteins. However, with the advent of high throughput proteomics to monitor protein-protein interactions at an organism level, we can now safely state that protein-protein interactions are the norm and not the exception. Thus, protein function must be understood in the larger context of the various binding complexes that each protein may form with interacting partners at a given time in the life cycle of a cell. Proteins are now seen as forming sophisticated interaction networks subject to remarkable regulation. The study of these interaction networks and regulatory mechanism, which I would like to term "systems proteomics," is one of the thriving fields of proteomics. The bird-eye view that systems proteomics offers should not however mask the fact that proteins are each characterized by a unique set of physical and chemical properties. In other words, no protein looks and behaves like another. This complicates enormously the design of high-throughput proteomics methods. Unlike genes, which, by and large, display similar physico-chemical behaviors and thus can be easily used in a high throughput mode, proteins are not easily amenable to the same treatment. It is thus important to remind researchers active in the proteomics field the fundamental basis of protein chemistry. This book attempts to bridge the two extreme ends of protein science: on one end, systems proteomics, which describes, at a system level, the intricate connection network that proteins form in a cell, and on the other end, protein chemistry and biophysics, which describe the molecular properties of individual proteins and the structural and thermodynamic basis of their interactions within the network. Br

Structural Bioinformatics Book

Structural Bioinformatics


  • Author : Jenny Gu
  • Publisher : John Wiley & Sons
  • Release Date : 2011-09-20
  • Genre: Science
  • Pages : 1064
  • ISBN 10 : 9781118210567

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Structural Bioinformatics Excerpt :

Structural Bioinformatics was the first major effort to showthe application of the principles and basic knowledge of the largerfield of bioinformatics to questions focusing on macromolecularstructure, such as the prediction of protein structure and howproteins carry out cellular functions, and how the application ofbioinformatics to these life science issues can improve healthcareby accelerating drug discovery and development. Designed primarilyas a reference, the first edition nevertheless saw widespread useas a textbook in graduate and undergraduate university coursesdealing with the theories and associated algorithms, resources, andtools used in the analysis, prediction, and theoreticalunderpinnings of DNA, RNA, and proteins. This new edition contains not only thorough updates of theadvances in structural bioinformatics since publication of thefirst edition, but also features eleven new chapters dealing withfrontier areas of high scientific impact, including: sampling andsearch techniques; use of mass spectrometry; genome functionalannotation; and much more. Offering detailed coverage for practitioners while remainingaccessible to the novice, Structural Bioinformatics, SecondEdition is a valuable resource and an excellent textbook for arange of readers in the bioinformatics and advanced biologyfields. Praise for the previous edition: "This book is a gold mine of fundamental and practicalinformation in an area not previously well represented in bookform." —Biochemistry and Molecular Education "... destined to become a classic reference work for workers atall levels in structural bioinformatics...recommended with greatenthusiasm for educators, researchers, and graduatestudents." —BAMBED "...a useful and timely summary of a rapidly expandingfield." —Nature Structural Biology "...a terrific job in this timely creation of a compilation ofarticles that appropriately addresses this issue." —Briefings in Bioinformatics

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.