protein-interaction books

Related books on 'protein-interaction'

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Protein Interaction Networks: Computational Analysis

by: Aidong Zhang
publisher: Cambridge University Press, published: 2009-04-06
ASIN: 0521888956
EAN: 9780521888950
sales rank: 782261
The analysis of protein-protein interactions is fundamental to the understanding of cellular organization, processes, and functions. Recent large-scale investigations of protein-protein interactions using such techniques as two-hybrid systems, mass spectrometry, and protein microarrays have enriched the available protein interaction data and facilitated the construction of integrated protein-protein interaction networks. The resulting large volume of protein-protein interaction data has posed a challenge to experimental investigation. This book provides a comprehensive understanding of the computational methods available for the analysis of protein-protein interaction networks. It offers an in-depth survey of a range of approaches, including statistical, topological, data-mining, and ontology-based methods. The author discusses the fundamental principles underlying each of these approaches and their respective benefits and drawbacks, and she offers suggestions for future research.

Introduction to Protein Science: Architecture, Function, and Genomics

by: Arthur M. Lesk
publisher: Oxford University Press, USA, published: 2010-05-20
ASIN: 0199541302
EAN: 9780199541300
sales rank: 173522
Designed for students in biology, biochemistry, and biomedicine, Introduction to Protein Science, Second Edition, provides a wide-ranging introduction to the contemporary study of proteins in health and disease. The text describes basic principles of protein structure and methods for studying them, illustrates the wide variety of functions that proteins have, and shows how their structures and functions are closely linked.

Introduction to Protein Science, Second Edition, relates the study of proteins to the context of modern high-throughput data streams of genomics and proteomics. It also provides a balanced treatment of the relationship between computational and experimental methods. The text is enhanced by marginal notes, exercises, problems, and "weblems" that develop students' database and computational server skills. An updated and expanded Companion Website offers resources for students and instructors.

New to this edition:

* Coverage of new developments in the field, including high-throughput methods
* A new chapter on enzyme kinetics
* Extended treatments of such topics as protein evolution and the immune system
* New pedagogical features including "key points" and "Proteins in Health and Disease" boxes
* New end-of-chapter exercises, problems, and "weblems"

Analysis of protein interaction networks using mass spectrometry compatible techniques [An article from: Analytica Chimica Acta]

by: M. Ethier
publisher: Elsevier, published: 2006-03-30
ASIN: B000PBZYVE
This digital document is a journal article from Analytica Chimica Acta, published by Elsevier in 2006. The article is delivered in HTML format and is available in your Amazon.com Media Library immediately after purchase. You can view it with any web browser.

Description:
The ability to map protein-protein interactions has grown tremendously over the last few years, making it possible to envision the mapping of whole or targeted protein interaction networks and to elucidate their temporal dynamics. The use of mass spectrometry for the study of protein complexes has proven to be an invaluable tool due to its ability to unambiguously identify proteins from a variety of biological samples. Furthermore, when affinity purification is combined with mass spectrometry analysis, the identification of multimeric protein complexes is greatly facilitated. Here, we review recent developments for the analysis of protein interaction networks by mass spectrometry and discuss the integration of different bioinformatic tools for predicting, validating, and managing interaction datasets.

Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids

by: Richard Durbin
publisher: Cambridge University Press, published: 1998-05-13
ASIN: 0521629713
EAN: 9780521629713
sales rank: 167077
Probablistic models are becoming increasingly important in analyzing 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 analyzing 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 is accessible to molecular biologists, computer scientists, and mathematicians with no formal knowledge of the other fields, and at the same time presents the state of the art in this new and important field.

DNA'Protein Interactions: Principles and Protocols (Methods in Molecular Biology)

publisher: Springer, published: 2012-03-31
ASIN: 1617371254
EAN: 9781617371257
sales rank: 11135181
Dr. Tom Moss assembles the new standard collection of cutting-edge techniques to identify key protein-DNA interactions and define their components, their manner of interaction, and their manner of function, both in the cell and in the test tube. The techniques span a wide range, from factor identification to atomic detail, and include multiple DNA footprinting analyses, including in vivo strategies, gel shift (EMSA) optimization, SELEX, surface plasmon resonance, site-specific DNA-protein crosslinking, and UV laser crosslinking. Comprehensive and broad ranging, DNA-Protein Interactions: Principles and Protocols, 2nd Edition, offers a stellar array of over 100 up-to-date and readily reproducible techniques that biochemists and molecular, cellular, and developmental biologists can use successfully today to understand DNA-protein interactions.

Proteins: Structure and Function

by: David Whitford
publisher: Wiley, published: 2005-05-23
ASIN: 0471498947
EAN: 9780471498940
sales rank: 368223
Proteins: Structure and Function is a comprehensive introduction to the study of proteins and their importance to modern biochemistry. Each chapter addresses the structure and function of proteins with a definitive theme designed to enhance student understanding. Opening with a brief historical overview of the subject the book moves on to discuss the ‘building blocks’ of proteins and their respective chemical and physical properties. Later chapters explore experimental and computational methods of comparing proteins, methods of protein purification and protein folding and stability.
The latest developments in the field are included and key concepts introduced in a user-friendly way to ensure that students are able to grasp the essentials before moving on to more advanced study and analysis of proteins.
An invaluable resource for students of Biochemistry, Molecular Biology, Medicine and Chemistry providing a modern approach to the subject of Proteins.

An Introduction to Tissue-Biomaterial Interactions

by: Kay C. Dee
publisher: Wiley-Liss, published: 2002-09-02
ASIN: 0471253944
EAN: 9780471253945
sales rank: 466394
An Introduction to Tissue-Biomaterial Interactions acquaints an undergraduate audience with the fundamental biological processes that influence these sophisticated, cutting-edge procedures. Chapters one through three provide more detail about the molecular-level events that happen at the tissue-implant interface, while chapters four through ten explore selected material, biological, and physiological consequences of these events. The importance of the body’s wound-healing response is emphasized throughout. Specific topics covered include:Structure and properties of biomaterials
Proteins
Protein-surface interactions
Blood-biomaterial interactions
Inflammation and infection
The immune system
Biomaterial responses to implantation
Biomaterial surface engineering
Intimal hyperplasia and osseointegration as examples of tissue-biomaterial interactions
The text also provides extensive coverage of the three pertinent interfaces between the body and the biomaterial, between the body and the living cells, and between the cells and the biomaterial that are critical in the development of tissue-engineered products that incorporate living cells within a biomaterial matrix. Ideal for a one-semester, biomedical engineering course, An Introduction to Tissue-Biomaterial Interactions provides a solid framework for understanding today’s and tomorrow’s implantable biomedical devices.

Protein, Protein Complexes: Analysis, Modeling and Drug Design

by: Martin Zacharias
publisher: Imperial College Press, published: 2010-05-04
ASIN: 1848163398
EAN: 9781848163393
sales rank: 1247680
Given the immense progress achieved in elucidating protein protein complex structures and in the field of protein interaction modeling, there is great demand for a book that gives interested researchers/students a comprehensive overview of the field. This book does just that. It focuses on what can be learned about protein protein interactions from the analysis of protein protein complex structures and interfaces. What are the driving forces for protein protein association? How can we extract the mechanism of specific recognition from studying protein protein interfaces? How can this knowledge be used to predict and design protein protein interactions (interaction regions and complex structures)? What methods are currently employed to design protein protein interactions, and how can we influence protein protein interactions by mutagenesis and small-molecule drugs or peptide mimetics?
The book consists of about 15 review chapters, written by experts, on the characterization of protein protein interfaces, structure determination of protein complexes (by NMR and X-ray), theory of protein protein binding, dynamics of protein interfaces, bioinformatics methods to predict interaction regions, and prediction of protein protein complex structures (docking and homology modeling of complexes, etc.) and design of protein protein interactions. It serves as a bridge between studying/analyzing protein protein complex structures (interfaces), predicting interactions, and influencing/designing interactions.

Prediction of Protein Structures, Functions, and Interactions

by: Janusz Bujnicki
publisher: Wiley, published: 2009-02-24
ASIN: 0470517670
EAN: 9780470517673
sales rank: 1592876
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.

Fundamentals of Protein NMR Spectroscopy (Focus on Structural Biology)

by: Gordon S. Rule
publisher: Springer, published: 2005-12-19
ASIN: 1402034997
EAN: 9781402034992
sales rank: 631190
NMR spectroscopy has proven to be a powerful technique to study the structure and dynamics of biological macromolecules. Fundamentals of Protein NMR Spectroscopy is a comprehensive textbook that guides the reader from a basic understanding of the phenomenological properties of magnetic resonance to the application and interpretation of modern multi-dimensional NMR experiments on 15N/13C-labeled proteins. Beginning with elementary quantum mechanics, a set of practical rules is presented and used to describe many commonly employed multi-dimensional, multi-nuclear NMR pulse sequences. A modular analysis of NMR pulse sequence building blocks also provides a basis for understanding and developing novel pulse programs. This text not only covers topics from chemical shift assignment to protein structure refinement, as well as the analysis of protein dynamics and chemical kinetics, but also provides a practical guide to many aspects of modern spectrometer hardware, sample preparation, experimental set-up, and data processing. End of chapter exercises are included to emphasize important concepts. Fundamentals of Protein NMR Spectroscopy not only offer students a systematic, in-depth, understanding of modern NMR spectroscopy and its application to biomolecular systems, but will also be a useful reference for the experienced investigator.

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	Protein Interaction Networks: Computational Analysis by: Aidong Zhang publisher: Cambridge University Press, published: 2009-04-06 ASIN: 0521888956 EAN: 9780521888950 sales rank: 782261 The analysis of protein-protein interactions is fundamental to the understanding of cellular organization, processes, and functions. Recent large-scale investigations of protein-protein interactions using such techniques as two-hybrid systems, mass spectrometry, and protein microarrays have enriched the available protein interaction data and facilitated the construction of integrated protein-protein interaction networks. The resulting large volume of protein-protein interaction data has posed a challenge to experimental investigation. This book provides a comprehensive understanding of the computational methods available for the analysis of protein-protein interaction networks. It offers an in-depth survey of a range of approaches, including statistical, topological, data-mining, and ontology-based methods. The author discusses the fundamental principles underlying each of these approaches and their respective benefits and drawbacks, and she offers suggestions for future research.
	Introduction to Protein Science: Architecture, Function, and Genomics by: Arthur M. Lesk publisher: Oxford University Press, USA, published: 2010-05-20 ASIN: 0199541302 EAN: 9780199541300 sales rank: 173522 Designed for students in biology, biochemistry, and biomedicine, Introduction to Protein Science, Second Edition, provides a wide-ranging introduction to the contemporary study of proteins in health and disease. The text describes basic principles of protein structure and methods for studying them, illustrates the wide variety of functions that proteins have, and shows how their structures and functions are closely linked. Introduction to Protein Science, Second Edition, relates the study of proteins to the context of modern high-throughput data streams of genomics and proteomics. It also provides a balanced treatment of the relationship between computational and experimental methods. The text is enhanced by marginal notes, exercises, problems, and "weblems" that develop students' database and computational server skills. An updated and expanded Companion Website offers resources for students and instructors. New to this edition: * Coverage of new developments in the field, including high-throughput methods * A new chapter on enzyme kinetics * Extended treatments of such topics as protein evolution and the immune system * New pedagogical features including "key points" and "Proteins in Health and Disease" boxes * New end-of-chapter exercises, problems, and "weblems"
	Analysis of protein interaction networks using mass spectrometry compatible techniques [An article from: Analytica Chimica Acta] by: M. Ethier publisher: Elsevier, published: 2006-03-30 ASIN: B000PBZYVE This digital document is a journal article from Analytica Chimica Acta, published by Elsevier in 2006. The article is delivered in HTML format and is available in your Amazon.com Media Library immediately after purchase. You can view it with any web browser. Description: The ability to map protein-protein interactions has grown tremendously over the last few years, making it possible to envision the mapping of whole or targeted protein interaction networks and to elucidate their temporal dynamics. The use of mass spectrometry for the study of protein complexes has proven to be an invaluable tool due to its ability to unambiguously identify proteins from a variety of biological samples. Furthermore, when affinity purification is combined with mass spectrometry analysis, the identification of multimeric protein complexes is greatly facilitated. Here, we review recent developments for the analysis of protein interaction networks by mass spectrometry and discuss the integration of different bioinformatic tools for predicting, validating, and managing interaction datasets.
	Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids by: Richard Durbin publisher: Cambridge University Press, published: 1998-05-13 ASIN: 0521629713 EAN: 9780521629713 sales rank: 167077 Probablistic models are becoming increasingly important in analyzing 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 analyzing 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 is accessible to molecular biologists, computer scientists, and mathematicians with no formal knowledge of the other fields, and at the same time presents the state of the art in this new and important field.
	DNA'Protein Interactions: Principles and Protocols (Methods in Molecular Biology) publisher: Springer, published: 2012-03-31 ASIN: 1617371254 EAN: 9781617371257 sales rank: 11135181 Dr. Tom Moss assembles the new standard collection of cutting-edge techniques to identify key protein-DNA interactions and define their components, their manner of interaction, and their manner of function, both in the cell and in the test tube. The techniques span a wide range, from factor identification to atomic detail, and include multiple DNA footprinting analyses, including in vivo strategies, gel shift (EMSA) optimization, SELEX, surface plasmon resonance, site-specific DNA-protein crosslinking, and UV laser crosslinking. Comprehensive and broad ranging, DNA-Protein Interactions: Principles and Protocols, 2nd Edition, offers a stellar array of over 100 up-to-date and readily reproducible techniques that biochemists and molecular, cellular, and developmental biologists can use successfully today to understand DNA-protein interactions.
	Proteins: Structure and Function by: David Whitford publisher: Wiley, published: 2005-05-23 ASIN: 0471498947 EAN: 9780471498940 sales rank: 368223 Proteins: Structure and Function is a comprehensive introduction to the study of proteins and their importance to modern biochemistry. Each chapter addresses the structure and function of proteins with a definitive theme designed to enhance student understanding. Opening with a brief historical overview of the subject the book moves on to discuss the ‘building blocks’ of proteins and their respective chemical and physical properties. Later chapters explore experimental and computational methods of comparing proteins, methods of protein purification and protein folding and stability. The latest developments in the field are included and key concepts introduced in a user-friendly way to ensure that students are able to grasp the essentials before moving on to more advanced study and analysis of proteins. An invaluable resource for students of Biochemistry, Molecular Biology, Medicine and Chemistry providing a modern approach to the subject of Proteins.
	An Introduction to Tissue-Biomaterial Interactions by: Kay C. Dee publisher: Wiley-Liss, published: 2002-09-02 ASIN: 0471253944 EAN: 9780471253945 sales rank: 466394 An Introduction to Tissue-Biomaterial Interactions acquaints an undergraduate audience with the fundamental biological processes that influence these sophisticated, cutting-edge procedures. Chapters one through three provide more detail about the molecular-level events that happen at the tissue-implant interface, while chapters four through ten explore selected material, biological, and physiological consequences of these events. The importance of the body’s wound-healing response is emphasized throughout. Specific topics covered include:Structure and properties of biomaterials Proteins Protein-surface interactions Blood-biomaterial interactions Inflammation and infection The immune system Biomaterial responses to implantation Biomaterial surface engineering Intimal hyperplasia and osseointegration as examples of tissue-biomaterial interactions The text also provides extensive coverage of the three pertinent interfaces between the body and the biomaterial, between the body and the living cells, and between the cells and the biomaterial that are critical in the development of tissue-engineered products that incorporate living cells within a biomaterial matrix. Ideal for a one-semester, biomedical engineering course, An Introduction to Tissue-Biomaterial Interactions provides a solid framework for understanding today’s and tomorrow’s implantable biomedical devices.
	Protein, Protein Complexes: Analysis, Modeling and Drug Design by: Martin Zacharias publisher: Imperial College Press, published: 2010-05-04 ASIN: 1848163398 EAN: 9781848163393 sales rank: 1247680 Given the immense progress achieved in elucidating protein protein complex structures and in the field of protein interaction modeling, there is great demand for a book that gives interested researchers/students a comprehensive overview of the field. This book does just that. It focuses on what can be learned about protein protein interactions from the analysis of protein protein complex structures and interfaces. What are the driving forces for protein protein association? How can we extract the mechanism of specific recognition from studying protein protein interfaces? How can this knowledge be used to predict and design protein protein interactions (interaction regions and complex structures)? What methods are currently employed to design protein protein interactions, and how can we influence protein protein interactions by mutagenesis and small-molecule drugs or peptide mimetics? The book consists of about 15 review chapters, written by experts, on the characterization of protein protein interfaces, structure determination of protein complexes (by NMR and X-ray), theory of protein protein binding, dynamics of protein interfaces, bioinformatics methods to predict interaction regions, and prediction of protein protein complex structures (docking and homology modeling of complexes, etc.) and design of protein protein interactions. It serves as a bridge between studying/analyzing protein protein complex structures (interfaces), predicting interactions, and influencing/designing interactions.
	Prediction of Protein Structures, Functions, and Interactions by: Janusz Bujnicki publisher: Wiley, published: 2009-02-24 ASIN: 0470517670 EAN: 9780470517673 sales rank: 1592876 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.
	Fundamentals of Protein NMR Spectroscopy (Focus on Structural Biology) by: Gordon S. Rule publisher: Springer, published: 2005-12-19 ASIN: 1402034997 EAN: 9781402034992 sales rank: 631190 NMR spectroscopy has proven to be a powerful technique to study the structure and dynamics of biological macromolecules. Fundamentals of Protein NMR Spectroscopy is a comprehensive textbook that guides the reader from a basic understanding of the phenomenological properties of magnetic resonance to the application and interpretation of modern multi-dimensional NMR experiments on 15N/13C-labeled proteins. Beginning with elementary quantum mechanics, a set of practical rules is presented and used to describe many commonly employed multi-dimensional, multi-nuclear NMR pulse sequences. A modular analysis of NMR pulse sequence building blocks also provides a basis for understanding and developing novel pulse programs. This text not only covers topics from chemical shift assignment to protein structure refinement, as well as the analysis of protein dynamics and chemical kinetics, but also provides a practical guide to many aspects of modern spectrometer hardware, sample preparation, experimental set-up, and data processing. End of chapter exercises are included to emphasize important concepts. Fundamentals of Protein NMR Spectroscopy not only offer students a systematic, in-depth, understanding of modern NMR spectroscopy and its application to biomolecular systems, but will also be a useful reference for the experienced investigator.