RNA Structure Determination

RNA Structure Determination

Author: Douglas H. Turner

Publisher: Humana

Published: 2016-09-24

Total Pages: 0

ISBN-13: 9781493964314

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This volume provides protocols and procedures for determining and modeling RNA structure. Chapters guide the reader through protocols for RNA secondary structure prediction, single sequence modeling, Crumple, RNAstructure to model conserved secondary structures with multiple homologs, the prediction of bimolecular secondary structures with RNAstructure, STarMir, protocols for structure mapping, mapping data to constrain or restrain RNA secondary structure prediction with RNAstructure, unassigned NMR resonances, modeling protocols for Rosetta FARFAR, RNAComposer , ModeRNA, and MC-Fold. 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 protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and Practical, RNA Structure Determination: Methods and Protocols aims to ensure successful results in the further study of this vital field.


Book Synopsis RNA Structure Determination by : Douglas H. Turner

Download or read book RNA Structure Determination written by Douglas H. Turner and published by Humana. This book was released on 2016-09-24 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume provides protocols and procedures for determining and modeling RNA structure. Chapters guide the reader through protocols for RNA secondary structure prediction, single sequence modeling, Crumple, RNAstructure to model conserved secondary structures with multiple homologs, the prediction of bimolecular secondary structures with RNAstructure, STarMir, protocols for structure mapping, mapping data to constrain or restrain RNA secondary structure prediction with RNAstructure, unassigned NMR resonances, modeling protocols for Rosetta FARFAR, RNAComposer , ModeRNA, and MC-Fold. 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 protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and Practical, RNA Structure Determination: Methods and Protocols aims to ensure successful results in the further study of this vital field.

RNA 3D Structure Analysis and Prediction

RNA 3D Structure Analysis and Prediction

Author: Neocles Leontis

Publisher: Springer Science & Business Media

Published: 2012-06-05

Total Pages: 402

ISBN-13: 3642257402

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With the dramatic increase in RNA 3D structure determination in recent years, we now know that RNA molecules are highly structured. Moreover, knowledge of RNA 3D structures has proven crucial for understanding in atomic detail how they carry out their biological functions. Because of the huge number of potentially important RNA molecules in biology, many more than can be studied experimentally, we need theoretical approaches for predicting 3D structures on the basis of sequences alone. This volume provides a comprehensive overview of current progress in the field by leading practitioners employing a variety of methods to model RNA 3D structures by homology, by fragment assembly, and by de novo energy and knowledge-based approaches.


Book Synopsis RNA 3D Structure Analysis and Prediction by : Neocles Leontis

Download or read book RNA 3D Structure Analysis and Prediction written by Neocles Leontis and published by Springer Science & Business Media. This book was released on 2012-06-05 with total page 402 pages. Available in PDF, EPUB and Kindle. Book excerpt: With the dramatic increase in RNA 3D structure determination in recent years, we now know that RNA molecules are highly structured. Moreover, knowledge of RNA 3D structures has proven crucial for understanding in atomic detail how they carry out their biological functions. Because of the huge number of potentially important RNA molecules in biology, many more than can be studied experimentally, we need theoretical approaches for predicting 3D structures on the basis of sequences alone. This volume provides a comprehensive overview of current progress in the field by leading practitioners employing a variety of methods to model RNA 3D structures by homology, by fragment assembly, and by de novo energy and knowledge-based approaches.

RNA Structure Determination: Methods and Protocols

RNA Structure Determination: Methods and Protocols

Author: Douglas H. Turner

Publisher: Methods in Molecular Biology

Published: 2018-10-08

Total Pages: 300

ISBN-13: 9781493981984

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This volume provides protocols and procedures for determining and modeling RNA structure. Chapters guide the reader through protocols for RNA secondary structure prediction, single sequence modeling, Crumple, RNAstructure to model conserved secondary structures with multiple homologs, the prediction of bimolecular secondary structures with RNAstructure, STarMir, protocols for structure mapping, mapping data to constrain or restrain RNA secondary structure prediction with RNAstructure, unassigned NMR resonances, modeling protocols for Rosetta FARFAR, RNAComposer, ModeRNA, and MC-Fold. 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 protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and Practical, RNA Structure Determination: Methods and Protocols aims to ensure successful results in the further study of this vital field.


Book Synopsis RNA Structure Determination: Methods and Protocols by : Douglas H. Turner

Download or read book RNA Structure Determination: Methods and Protocols written by Douglas H. Turner and published by Methods in Molecular Biology. This book was released on 2018-10-08 with total page 300 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume provides protocols and procedures for determining and modeling RNA structure. Chapters guide the reader through protocols for RNA secondary structure prediction, single sequence modeling, Crumple, RNAstructure to model conserved secondary structures with multiple homologs, the prediction of bimolecular secondary structures with RNAstructure, STarMir, protocols for structure mapping, mapping data to constrain or restrain RNA secondary structure prediction with RNAstructure, unassigned NMR resonances, modeling protocols for Rosetta FARFAR, RNAComposer, ModeRNA, and MC-Fold. 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 protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and Practical, RNA Structure Determination: Methods and Protocols aims to ensure successful results in the further study of this vital field.

RNA Sequence, Structure, and Function: Computational and Bioinformatic Methods

RNA Sequence, Structure, and Function: Computational and Bioinformatic Methods

Author: Jan Gorodkin

Publisher: Humana

Published: 2014-03-18

Total Pages: 0

ISBN-13: 9781627037082

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The existence of genes for RNA molecules not coding for proteins (ncRNAs) has been recognized since the 1950's, but until recently, aside from the critically important ribosomal and transfer RNA genes, most focus has been on protein coding genes. However, a long series of striking discoveries, from RNA's ability to carry out catalytic function, to discovery of riboswitches, microRNAs and other ribo-regulators performing critical tasks in essentially all living organisms, has created a burgeoning interest in this primordial component of the biosphere. However, the structural characteristics and evolutionary constraints on RNA molecules are very different from those of proteins, necessitating development of a completely new suite of informatic tools to address these challenges. In RNA Sequence, Structure, Function: Computational and Bioinformatic Methods, expert researchers in the field describe a substantial and relevant fraction of these methodologies from both practical and computational/algorithmic perspectives. Focusing on both of these directions addresses both the biologist interested in knowing more about RNA bioinformatics as well as the bioinformaticist interested in more detailed aspects of the algorithms. Written in the highly successful Methods in Molecular Biology series format, the chapters include the kind of detailed description and implementation advice that is crucial for getting optimal results. Thorough and intuitive, RNA Sequence, Structure, Function: Computational and Bioinformatic Methods aids scientists in continuing to study key methods and principles of RNA bioinformatics.


Book Synopsis RNA Sequence, Structure, and Function: Computational and Bioinformatic Methods by : Jan Gorodkin

Download or read book RNA Sequence, Structure, and Function: Computational and Bioinformatic Methods written by Jan Gorodkin and published by Humana. This book was released on 2014-03-18 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: The existence of genes for RNA molecules not coding for proteins (ncRNAs) has been recognized since the 1950's, but until recently, aside from the critically important ribosomal and transfer RNA genes, most focus has been on protein coding genes. However, a long series of striking discoveries, from RNA's ability to carry out catalytic function, to discovery of riboswitches, microRNAs and other ribo-regulators performing critical tasks in essentially all living organisms, has created a burgeoning interest in this primordial component of the biosphere. However, the structural characteristics and evolutionary constraints on RNA molecules are very different from those of proteins, necessitating development of a completely new suite of informatic tools to address these challenges. In RNA Sequence, Structure, Function: Computational and Bioinformatic Methods, expert researchers in the field describe a substantial and relevant fraction of these methodologies from both practical and computational/algorithmic perspectives. Focusing on both of these directions addresses both the biologist interested in knowing more about RNA bioinformatics as well as the bioinformaticist interested in more detailed aspects of the algorithms. Written in the highly successful Methods in Molecular Biology series format, the chapters include the kind of detailed description and implementation advice that is crucial for getting optimal results. Thorough and intuitive, RNA Sequence, Structure, Function: Computational and Bioinformatic Methods aids scientists in continuing to study key methods and principles of RNA bioinformatics.

Handbook of RNA Biochemistry

Handbook of RNA Biochemistry

Author: Roland K. Hartmann

Publisher: John Wiley & Sons

Published: 2015-06-22

Total Pages: 1370

ISBN-13: 3527327762

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The second edition of a highly acclaimed handbook and ready reference. Unmatched in its breadth and quality, around 100 specialists from all over the world share their up-to-date expertise and experiences, including hundreds of protocols, complete with explanations, and hitherto unpublished troubleshooting hints. They cover all modern techniques for the handling, analysis and modification of RNAs and their complexes with proteins. Throughout, they bear the practising bench scientist in mind, providing quick and reliable access to a plethora of solutions for practical questions of RNA research, ranging from simple to highly complex. This broad scope allows the treatment of specialized methods side by side with basic biochemical techniques, making the book a real treasure trove for every researcher experimenting with RNA.


Book Synopsis Handbook of RNA Biochemistry by : Roland K. Hartmann

Download or read book Handbook of RNA Biochemistry written by Roland K. Hartmann and published by John Wiley & Sons. This book was released on 2015-06-22 with total page 1370 pages. Available in PDF, EPUB and Kindle. Book excerpt: The second edition of a highly acclaimed handbook and ready reference. Unmatched in its breadth and quality, around 100 specialists from all over the world share their up-to-date expertise and experiences, including hundreds of protocols, complete with explanations, and hitherto unpublished troubleshooting hints. They cover all modern techniques for the handling, analysis and modification of RNAs and their complexes with proteins. Throughout, they bear the practising bench scientist in mind, providing quick and reliable access to a plethora of solutions for practical questions of RNA research, ranging from simple to highly complex. This broad scope allows the treatment of specialized methods side by side with basic biochemical techniques, making the book a real treasure trove for every researcher experimenting with RNA.

RNA Structure and Folding

RNA Structure and Folding

Author: Dagmar Klostermeier

Publisher: Walter de Gruyter

Published: 2013-10-14

Total Pages: 432

ISBN-13: 3110284952

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While structure-function relationships of proteins have been studied for a long time, structural studies of RNA face additional challenges. Nevertheless, with the continuous discovery of novel RNA molecules with key cellular functions and of novel pathways and interaction networks, the need for structural information of RNA is still increasing. This volume provides an introduction into techniques to assess structure and folding of RNA. Each chapter explains the theoretical background of one technique, and illustrates possibilities and limitations in selected application examples.


Book Synopsis RNA Structure and Folding by : Dagmar Klostermeier

Download or read book RNA Structure and Folding written by Dagmar Klostermeier and published by Walter de Gruyter. This book was released on 2013-10-14 with total page 432 pages. Available in PDF, EPUB and Kindle. Book excerpt: While structure-function relationships of proteins have been studied for a long time, structural studies of RNA face additional challenges. Nevertheless, with the continuous discovery of novel RNA molecules with key cellular functions and of novel pathways and interaction networks, the need for structural information of RNA is still increasing. This volume provides an introduction into techniques to assess structure and folding of RNA. Each chapter explains the theoretical background of one technique, and illustrates possibilities and limitations in selected application examples.

Bioinformatics

Bioinformatics

Author: Jonathan M. Keith

Publisher: Humana

Published: 2018-06-21

Total Pages: 491

ISBN-13: 9781493982523

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This second edition provides updated and expanded chapters covering a broad sampling of useful and current methods in the rapidly developing and expanding field of bioinformatics. Bioinformatics, Volume I: Data, Sequence Analysis, and Evolution, Second Edition is comprised of three sections: Data and Databases, Sequence Analysis, and Phylogenetics and Evolution. The first section details bioinformatics methodologies in the generation of sequence and structural data and its organization into conceptual categories, and databases to facilitate further analyses. The Sequence Analysis section describes the fundamental methodologies for processing the sequences of biological molecules: techniques that are used in almost every pipeline of bioinformatics analysis, particularly in the preliminary stages of such pipelines. Last but not least, the phylogenetics and evolution section deals with methodologies that compare biological sequences for the purpose of understanding how they evolved. As a volume in the highly successful Methods in Molecular Biology series, chapters feature the kind of detail and expert implementation advice to ensure positive results. Comprehensive and practical, Bioinformatics, Volume I: Data, Sequence Analysis, and Evolution, Second Edition is an essential resource for graduate students, early career researchers, and others who are in the process of integrating new bioinformatics methods into their research.


Book Synopsis Bioinformatics by : Jonathan M. Keith

Download or read book Bioinformatics written by Jonathan M. Keith and published by Humana. This book was released on 2018-06-21 with total page 491 pages. Available in PDF, EPUB and Kindle. Book excerpt: This second edition provides updated and expanded chapters covering a broad sampling of useful and current methods in the rapidly developing and expanding field of bioinformatics. Bioinformatics, Volume I: Data, Sequence Analysis, and Evolution, Second Edition is comprised of three sections: Data and Databases, Sequence Analysis, and Phylogenetics and Evolution. The first section details bioinformatics methodologies in the generation of sequence and structural data and its organization into conceptual categories, and databases to facilitate further analyses. The Sequence Analysis section describes the fundamental methodologies for processing the sequences of biological molecules: techniques that are used in almost every pipeline of bioinformatics analysis, particularly in the preliminary stages of such pipelines. Last but not least, the phylogenetics and evolution section deals with methodologies that compare biological sequences for the purpose of understanding how they evolved. As a volume in the highly successful Methods in Molecular Biology series, chapters feature the kind of detail and expert implementation advice to ensure positive results. Comprehensive and practical, Bioinformatics, Volume I: Data, Sequence Analysis, and Evolution, Second Edition is an essential resource for graduate students, early career researchers, and others who are in the process of integrating new bioinformatics methods into their research.

RNA Structure Prediction

RNA Structure Prediction

Author: Risa Karakida Kawaguchi

Publisher: Springer Nature

Published: 2023-01-27

Total Pages: 304

ISBN-13: 1071627686

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This book explores recent progress in RNA secondary, tertiary structure prediction, and its application from an expansive point of view. Because of advancements in experimental protocols and devices, the integration of new types of data as well as new analysis techniques is necessary, and this volume discusses additional topics that are closely related to RNA structure prediction, such as the detection of structure-disrupting mutations, high-throughput structure analysis, and 3D structure design. Written for the highly successful Methods in Molecular Biology series, chapters feature the kind of detailed implementation advice that leads to quality research results. Authoritative and practical, RNA Structure Prediction serves as a valuable guide for both experimental and computational RNA researchers.


Book Synopsis RNA Structure Prediction by : Risa Karakida Kawaguchi

Download or read book RNA Structure Prediction written by Risa Karakida Kawaguchi and published by Springer Nature. This book was released on 2023-01-27 with total page 304 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book explores recent progress in RNA secondary, tertiary structure prediction, and its application from an expansive point of view. Because of advancements in experimental protocols and devices, the integration of new types of data as well as new analysis techniques is necessary, and this volume discusses additional topics that are closely related to RNA structure prediction, such as the detection of structure-disrupting mutations, high-throughput structure analysis, and 3D structure design. Written for the highly successful Methods in Molecular Biology series, chapters feature the kind of detailed implementation advice that leads to quality research results. Authoritative and practical, RNA Structure Prediction serves as a valuable guide for both experimental and computational RNA researchers.

RNA-ligand Interactions: Structural biology methods. Semisynthetic methodologies ; RNA structure determination ; Techniques for monitoring RNA conformation and dynamics ; Modeling tertiary structure

RNA-ligand Interactions: Structural biology methods. Semisynthetic methodologies ; RNA structure determination ; Techniques for monitoring RNA conformation and dynamics ; Modeling tertiary structure

Author: Daniel Walter Celander

Publisher:

Published: 2000

Total Pages: 602

ISBN-13:

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Book Synopsis RNA-ligand Interactions: Structural biology methods. Semisynthetic methodologies ; RNA structure determination ; Techniques for monitoring RNA conformation and dynamics ; Modeling tertiary structure by : Daniel Walter Celander

Download or read book RNA-ligand Interactions: Structural biology methods. Semisynthetic methodologies ; RNA structure determination ; Techniques for monitoring RNA conformation and dynamics ; Modeling tertiary structure written by Daniel Walter Celander and published by . This book was released on 2000 with total page 602 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Structural Bioinformatics

Structural Bioinformatics

Author: Jenny Gu

Publisher: John Wiley & Sons

Published: 2011-09-20

Total Pages: 1105

ISBN-13: 1118210565

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Structural Bioinformatics was the first major effort to show the application of the principles and basic knowledge of the larger field of bioinformatics to questions focusing on macromolecular structure, such as the prediction of protein structure and how proteins carry out cellular functions, and how the application of bioinformatics to these life science issues can improve healthcare by accelerating drug discovery and development. Designed primarily as a reference, the first edition nevertheless saw widespread use as a textbook in graduate and undergraduate university courses dealing with the theories and associated algorithms, resources, and tools used in the analysis, prediction, and theoretical underpinnings of DNA, RNA, and proteins. This new edition contains not only thorough updates of the advances in structural bioinformatics since publication of the first edition, but also features eleven new chapters dealing with frontier areas of high scientific impact, including: sampling and search techniques; use of mass spectrometry; genome functional annotation; and much more. Offering detailed coverage for practitioners while remaining accessible to the novice, Structural Bioinformatics, Second Edition is a valuable resource and an excellent textbook for a range of readers in the bioinformatics and advanced biology fields. Praise for the previous edition: "This book is a gold mine of fundamental and practical information in an area not previously well represented in book form." —Biochemistry and Molecular Education "... destined to become a classic reference work for workers at all levels in structural bioinformatics...recommended with great enthusiasm for educators, researchers, and graduate students." —BAMBED "...a useful and timely summary of a rapidly expanding field." —Nature Structural Biology "...a terrific job in this timely creation of a compilation of articles that appropriately addresses this issue." —Briefings in Bioinformatics


Book Synopsis Structural Bioinformatics by : Jenny Gu

Download or read book Structural Bioinformatics written by Jenny Gu and published by John Wiley & Sons. This book was released on 2011-09-20 with total page 1105 pages. Available in PDF, EPUB and Kindle. Book excerpt: Structural Bioinformatics was the first major effort to show the application of the principles and basic knowledge of the larger field of bioinformatics to questions focusing on macromolecular structure, such as the prediction of protein structure and how proteins carry out cellular functions, and how the application of bioinformatics to these life science issues can improve healthcare by accelerating drug discovery and development. Designed primarily as a reference, the first edition nevertheless saw widespread use as a textbook in graduate and undergraduate university courses dealing with the theories and associated algorithms, resources, and tools used in the analysis, prediction, and theoretical underpinnings of DNA, RNA, and proteins. This new edition contains not only thorough updates of the advances in structural bioinformatics since publication of the first edition, but also features eleven new chapters dealing with frontier areas of high scientific impact, including: sampling and search techniques; use of mass spectrometry; genome functional annotation; and much more. Offering detailed coverage for practitioners while remaining accessible to the novice, Structural Bioinformatics, Second Edition is a valuable resource and an excellent textbook for a range of readers in the bioinformatics and advanced biology fields. Praise for the previous edition: "This book is a gold mine of fundamental and practical information in an area not previously well represented in book form." —Biochemistry and Molecular Education "... destined to become a classic reference work for workers at all levels in structural bioinformatics...recommended with great enthusiasm for educators, researchers, and graduate students." —BAMBED "...a useful and timely summary of a rapidly expanding field." —Nature Structural Biology "...a terrific job in this timely creation of a compilation of articles that appropriately addresses this issue." —Briefings in Bioinformatics