Prediction of Protein Structure and the Principles of Protein Conformation

Prediction of Protein Structure and the Principles of Protein Conformation

Author: G.D. Fasman

Publisher: Springer Science & Business Media

Published: 2012-12-06

Total Pages: 796

ISBN-13: 1461315719

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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.


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.

Principles of Protein Structure

Principles of Protein Structure

Author: G.E. Schulz

Publisher: Springer Science & Business Media

Published: 2013-12-01

Total Pages: 328

ISBN-13: 1461261376

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New textbooks at all levels of chemistry appear with great regularity. Some fields like basic biochemistry, organic reaction mechanisms, and chemical thermodynamics are well represented by many excellent texts, and new or revised editions are published sufficiently often to keep up with progress in research. However, some areas of chemistry, especially many of those taught at the graduate level, suffer from a real lack of up-to-date textbooks. The most serious needs occur in fields that are rapidly changing. Textbooks in these subjects usually have to be written by scientists actually involved in the research which is advancing the field. It is not often easy to persuade such individuals to set time aside to help spread the knowledge they have accumulated. Our goal, in this series, is to pinpoint areas of chemistry where recent progress has outpaced what is covered in any available textbooks, and then seek out and persuade experts in these fields to produce relatively concise but instructive introductions to their fields. These should serve the needs of one semester or one quarter graduate courses in chemistry and biochemistry. In some cases the availability of texts in active research areas should help stimulate the creation of new courses.


Book Synopsis Principles of Protein Structure by : G.E. Schulz

Download or read book Principles of Protein Structure written by G.E. Schulz and published by Springer Science & Business Media. This book was released on 2013-12-01 with total page 328 pages. Available in PDF, EPUB and Kindle. Book excerpt: New textbooks at all levels of chemistry appear with great regularity. Some fields like basic biochemistry, organic reaction mechanisms, and chemical thermodynamics are well represented by many excellent texts, and new or revised editions are published sufficiently often to keep up with progress in research. However, some areas of chemistry, especially many of those taught at the graduate level, suffer from a real lack of up-to-date textbooks. The most serious needs occur in fields that are rapidly changing. Textbooks in these subjects usually have to be written by scientists actually involved in the research which is advancing the field. It is not often easy to persuade such individuals to set time aside to help spread the knowledge they have accumulated. Our goal, in this series, is to pinpoint areas of chemistry where recent progress has outpaced what is covered in any available textbooks, and then seek out and persuade experts in these fields to produce relatively concise but instructive introductions to their fields. These should serve the needs of one semester or one quarter graduate courses in chemistry and biochemistry. In some cases the availability of texts in active research areas should help stimulate the creation of new courses.

The Protein Folding Problem and Tertiary Structure Prediction

The Protein Folding Problem and Tertiary Structure Prediction

Author: Kenneth M.Jr. Merz

Publisher: Springer Science & Business Media

Published: 2012-12-06

Total Pages: 585

ISBN-13: 1468468316

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A solution to the protein folding problem has eluded researchers for more than 30 years. The stakes are high. Such a solution will make 40,000 more tertiary structures available for immediate study by translating the DNA sequence information in the sequence databases into three-dimensional protein structures. This translation will be indispensable for the analy sis of results from the Human Genome Project, de novo protein design, and many other areas of biotechnological research. Finally, an in-depth study of the rules of protein folding should provide vital clues to the protein fold ing process. The search for these rules is therefore an important objective for theoretical molecular biology. Both experimental and theoretical ap proaches have been used in the search for a solution, with many promising results but no general solution. In recent years, there has been an exponen tial increase in the power of computers. This has triggered an incredible outburst of theoretical approaches to solving the protein folding problem ranging from molecular dynamics-based studies of proteins in solution to the actual prediction of protein structures from first principles. This volume attempts to present a concise overview of these advances. Adrian Roitberg and Ron Elber describe the locally enhanced sam pling/simulated annealing conformational search algorithm (Chapter 1), which is potentially useful for the rapid conformational search of larger molecular systems.


Book Synopsis The Protein Folding Problem and Tertiary Structure Prediction by : Kenneth M.Jr. Merz

Download or read book The Protein Folding Problem and Tertiary Structure Prediction written by Kenneth M.Jr. Merz and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 585 pages. Available in PDF, EPUB and Kindle. Book excerpt: A solution to the protein folding problem has eluded researchers for more than 30 years. The stakes are high. Such a solution will make 40,000 more tertiary structures available for immediate study by translating the DNA sequence information in the sequence databases into three-dimensional protein structures. This translation will be indispensable for the analy sis of results from the Human Genome Project, de novo protein design, and many other areas of biotechnological research. Finally, an in-depth study of the rules of protein folding should provide vital clues to the protein fold ing process. The search for these rules is therefore an important objective for theoretical molecular biology. Both experimental and theoretical ap proaches have been used in the search for a solution, with many promising results but no general solution. In recent years, there has been an exponen tial increase in the power of computers. This has triggered an incredible outburst of theoretical approaches to solving the protein folding problem ranging from molecular dynamics-based studies of proteins in solution to the actual prediction of protein structures from first principles. This volume attempts to present a concise overview of these advances. Adrian Roitberg and Ron Elber describe the locally enhanced sam pling/simulated annealing conformational search algorithm (Chapter 1), which is potentially useful for the rapid conformational search of larger molecular systems.

Protein Structure Prediction : A Practical Approach

Protein Structure Prediction : A Practical Approach

Author: Michael J. E. Sternberg

Publisher: Oxford University Press, USA

Published: 1996-11-28

Total Pages: 322

ISBN-13: 0191588997

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The three-dimensional structure of proteins is a key factor in their biological activity. There is an increasing need to be able to predict the structure of a protein once its amino-acid sequence is known; this book presents practical methods of achieving that ambitious aim, using the latest computer modelling algorithms. - ;The prediction of the three-dimensional structure of a protein from its sequence is a problem faced by an ever-increasing number of biological scientists as they strive to utilize genetic information. The increasing sizes of the sequence and structural databases, the improvements in computing power, and the deeper understanding of the principles of protein structure have led to major developments in the field in the last few years. This book presents practical computer-based methods using the latest computer modelling algorithms. -


Book Synopsis Protein Structure Prediction : A Practical Approach by : Michael J. E. Sternberg

Download or read book Protein Structure Prediction : A Practical Approach written by Michael J. E. Sternberg and published by Oxford University Press, USA. This book was released on 1996-11-28 with total page 322 pages. Available in PDF, EPUB and Kindle. Book excerpt: The three-dimensional structure of proteins is a key factor in their biological activity. There is an increasing need to be able to predict the structure of a protein once its amino-acid sequence is known; this book presents practical methods of achieving that ambitious aim, using the latest computer modelling algorithms. - ;The prediction of the three-dimensional structure of a protein from its sequence is a problem faced by an ever-increasing number of biological scientists as they strive to utilize genetic information. The increasing sizes of the sequence and structural databases, the improvements in computing power, and the deeper understanding of the principles of protein structure have led to major developments in the field in the last few years. This book presents practical computer-based methods using the latest computer modelling algorithms. -

Protein Engineering

Protein Engineering

Author: Jeffrey L. Cleland

Publisher: Wiley-Liss

Published: 1996-02-07

Total Pages: 558

ISBN-13:

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PROTEIN ENGINEERING Principles and Practice Edited by JEFFREY L. CLELAND CHARLES S. CRAIK Proteins are involved in every aspect of life-structure, motion, catalysis, recognition and regulation. Protein Engineering: Principles and Practice provides a basic framework for understanding both proteins and protein engineering. This comprehensive book covers general, yet essential knowledge required for successful protein engineering, including everything from the fundamentals to modifying existing proteins and developing new proteins. The book begins by introducing the main concepts of protein engineering, including: understanding protein conformation, comprehending the relationship between protein composition and structure, and potential methods for predicting a protein's conformation. Other major subjects addressed are: * Using different host cell expression systems to produce specific proteins * Protein folding * Structure and function of proteins in relation to drug design * Construction of synthetic metal binding sites in proteins * Manufacture of tissue plasminogen activator * Generation of therapeutic antibodies This broad range of topics provides a solid foundation in protein engineering and supplies readers with knowledge essential to the design and production of proteins. Of primary interest to protein scientists-both students and researchers, in academia as well as industry-Protein Engineering is also extremely useful to chemical engineers, protein chemists, biochemists, and pharmaceutical chemists.


Book Synopsis Protein Engineering by : Jeffrey L. Cleland

Download or read book Protein Engineering written by Jeffrey L. Cleland and published by Wiley-Liss. This book was released on 1996-02-07 with total page 558 pages. Available in PDF, EPUB and Kindle. Book excerpt: PROTEIN ENGINEERING Principles and Practice Edited by JEFFREY L. CLELAND CHARLES S. CRAIK Proteins are involved in every aspect of life-structure, motion, catalysis, recognition and regulation. Protein Engineering: Principles and Practice provides a basic framework for understanding both proteins and protein engineering. This comprehensive book covers general, yet essential knowledge required for successful protein engineering, including everything from the fundamentals to modifying existing proteins and developing new proteins. The book begins by introducing the main concepts of protein engineering, including: understanding protein conformation, comprehending the relationship between protein composition and structure, and potential methods for predicting a protein's conformation. Other major subjects addressed are: * Using different host cell expression systems to produce specific proteins * Protein folding * Structure and function of proteins in relation to drug design * Construction of synthetic metal binding sites in proteins * Manufacture of tissue plasminogen activator * Generation of therapeutic antibodies This broad range of topics provides a solid foundation in protein engineering and supplies readers with knowledge essential to the design and production of proteins. Of primary interest to protein scientists-both students and researchers, in academia as well as industry-Protein Engineering is also extremely useful to chemical engineers, protein chemists, biochemists, and pharmaceutical chemists.

Protein Folding in Silico

Protein Folding in Silico

Author: Irena Roterman-Konieczna

Publisher: Elsevier

Published: 2012-10-04

Total Pages: 241

ISBN-13: 1908818255

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Protein folding is a process by which a protein structure assumes its functional shape of conformation, and has been the subject of research since the publication of the first software tool for protein structure prediction. Protein folding in silico approaches this issue by introducing an ab initio model that attempts to simulate as far as possible the folding process as it takes place in vivo, and attempts to construct a mechanistic model on the basis of the predictions made. The opening chapters discuss the early stage intermediate and late stage intermediate models, followed by a discussion of structural information that affects the interpretation of the folding process. The second half of the book covers a variety of topics including ligand binding site recognition, the "fuzzy oil drop" model and its use in simulation of the polypeptide chain, and misfolded proteins. The book ends with an overview of a number of other ab initio methods for protein structure predictions and some concluding remarks. Discusses a range of ab initio models for protein structure prediction Introduces a unique model based on experimental observations Describes various methods for the quantitative assessment of the presented models from the viewpoint of information theory


Book Synopsis Protein Folding in Silico by : Irena Roterman-Konieczna

Download or read book Protein Folding in Silico written by Irena Roterman-Konieczna and published by Elsevier. This book was released on 2012-10-04 with total page 241 pages. Available in PDF, EPUB and Kindle. Book excerpt: Protein folding is a process by which a protein structure assumes its functional shape of conformation, and has been the subject of research since the publication of the first software tool for protein structure prediction. Protein folding in silico approaches this issue by introducing an ab initio model that attempts to simulate as far as possible the folding process as it takes place in vivo, and attempts to construct a mechanistic model on the basis of the predictions made. The opening chapters discuss the early stage intermediate and late stage intermediate models, followed by a discussion of structural information that affects the interpretation of the folding process. The second half of the book covers a variety of topics including ligand binding site recognition, the "fuzzy oil drop" model and its use in simulation of the polypeptide chain, and misfolded proteins. The book ends with an overview of a number of other ab initio methods for protein structure predictions and some concluding remarks. Discusses a range of ab initio models for protein structure prediction Introduces a unique model based on experimental observations Describes various methods for the quantitative assessment of the presented models from the viewpoint of information theory

Protein Conformation

Protein Conformation

Author: Linda B. Roswell

Publisher: Nova Publishers

Published: 2008

Total Pages: 280

ISBN-13: 9781604562194

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Protein structure is the characteristic 3-dimensional shape of a protein, imposed upon it by the secondary and tertiary structure of the peptide chain. This stage in the structure of a protein describes the highest level of organisation in overall structure assumed by multimeric proteins (aggregates of more than one polypeptide chain). This is the fourth folding level of protein building. This new book presents the latest research in the field.


Book Synopsis Protein Conformation by : Linda B. Roswell

Download or read book Protein Conformation written by Linda B. Roswell and published by Nova Publishers. This book was released on 2008 with total page 280 pages. Available in PDF, EPUB and Kindle. Book excerpt: Protein structure is the characteristic 3-dimensional shape of a protein, imposed upon it by the secondary and tertiary structure of the peptide chain. This stage in the structure of a protein describes the highest level of organisation in overall structure assumed by multimeric proteins (aggregates of more than one polypeptide chain). This is the fourth folding level of protein building. This new book presents the latest research in the field.

Protein Conformation

Protein Conformation

Author: Derek J. Chadwick

Publisher: John Wiley & Sons

Published: 2008-04-30

Total Pages: 282

ISBN-13: 0470514159

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How the amino acid sequence of a protein determines its three-dimensional structure is a major problem in biology and chemistry. Leading experts in the fields of NMR spectroscopy, X-ray crystallography, protein engineering and molecular modeling offer provocative insights into current views on the protein folding problem and various aspects for future progress.


Book Synopsis Protein Conformation by : Derek J. Chadwick

Download or read book Protein Conformation written by Derek J. Chadwick and published by John Wiley & Sons. This book was released on 2008-04-30 with total page 282 pages. Available in PDF, EPUB and Kindle. Book excerpt: How the amino acid sequence of a protein determines its three-dimensional structure is a major problem in biology and chemistry. Leading experts in the fields of NMR spectroscopy, X-ray crystallography, protein engineering and molecular modeling offer provocative insights into current views on the protein folding problem and various aspects for future progress.

Protein Folding

Protein Folding

Author: Charis Ghelis

Publisher: Academic Press

Published: 2012-12-02

Total Pages: 580

ISBN-13: 0323140920

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Protein Folding aims to collect the most important information in the field of protein folding and probes the main principles that govern formation of the three-dimensional structure of a protein from a nascent polypeptide chain, as well as how the functional properties appear. This text is organized into three sections and consists of 15 chapters. After an introductory chapter where the main problems of protein folding are considered at the cellular level in the context of protein biosynthesis, the discussion turns to the conformation of native globular proteins. Definitions and rules of nomenclature are given, including the structural organization of globular proteins deduced from X-ray crystallographic data. Folding mechanisms are tentatively deduced from the observation of invariants in the architecture of folded proteins. The next chapters focus on the energetics of protein conformation and structure, indicating the principles of thermodynamic stability of the native structure, along with theoretical computation studies of protein folding, structure prediction, and folding simulation. The reader is also introduced to various experimental approaches; the reversibility of the unfolding-folding process; equilibrium and kinetic studies; and detection and characterization of intermediates in protein folding. This text concludes with a chapter dealing with problems specific to oligomeric proteins. This book is intended for research scientists, specialists, biochemists, and students of biochemistry and biology.


Book Synopsis Protein Folding by : Charis Ghelis

Download or read book Protein Folding written by Charis Ghelis and published by Academic Press. This book was released on 2012-12-02 with total page 580 pages. Available in PDF, EPUB and Kindle. Book excerpt: Protein Folding aims to collect the most important information in the field of protein folding and probes the main principles that govern formation of the three-dimensional structure of a protein from a nascent polypeptide chain, as well as how the functional properties appear. This text is organized into three sections and consists of 15 chapters. After an introductory chapter where the main problems of protein folding are considered at the cellular level in the context of protein biosynthesis, the discussion turns to the conformation of native globular proteins. Definitions and rules of nomenclature are given, including the structural organization of globular proteins deduced from X-ray crystallographic data. Folding mechanisms are tentatively deduced from the observation of invariants in the architecture of folded proteins. The next chapters focus on the energetics of protein conformation and structure, indicating the principles of thermodynamic stability of the native structure, along with theoretical computation studies of protein folding, structure prediction, and folding simulation. The reader is also introduced to various experimental approaches; the reversibility of the unfolding-folding process; equilibrium and kinetic studies; and detection and characterization of intermediates in protein folding. This text concludes with a chapter dealing with problems specific to oligomeric proteins. This book is intended for research scientists, specialists, biochemists, and students of biochemistry and biology.

Protein Structure Prediction

Protein Structure Prediction

Author: David Webster

Publisher: Springer Science & Business Media

Published: 2008-02-03

Total Pages: 425

ISBN-13: 1592593682

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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.


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.