Molecular Dynamics And Quantum Mechanics Studies Of Rna Structures

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Molecular Dynamics and Quantum Mechanics Studies of RNA Structures

Author : Jianbo Zhao
Publisher :
ISBN 13 :
Total Pages : 108 pages
Book Rating : 4.:/5 (123 download)

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Book Synopsis Molecular Dynamics and Quantum Mechanics Studies of RNA Structures by : Jianbo Zhao

Download or read book Molecular Dynamics and Quantum Mechanics Studies of RNA Structures written by Jianbo Zhao and published by . This book was released on 2020 with total page 108 pages. Available in PDF, EPUB and Kindle. Book excerpt: "Determining and predicting 3D structure and dynamics for RNA is challenging, but can reveal structure-function relationships and facilitate design of therapeutics. Computational models can predict the structure, energetics, and dynamics of RNA in an inexpensive and efficient way. In chapter 2, nuclear magnetic resonance spectra for RNA and DNA single strands, CAAU and UCAAUC, are used as benchmarks to test molecular dynamics simulations, AMBER force fields OL3 and ROC-RNA were used for RNA and BSC1 for DNA. A detailed scheme for making comparisons is also presented; however, an improved RNA force field is needed to accurately model single strands, especially terminal nucleotides. In chapter 3, quantum mechanics models for nucleobases were studied. Optimized geometries were compared to the small molecule crystal structures in the Cambridge Structural Database. The results showed QM can provide reliable geometrical restraints for both isolated and paired bases"--Page viii.

Computational studies of RNA and DNA

Author : Jirí Šponer
Publisher : Springer Science & Business Media
ISBN 13 : 1402048513
Total Pages : 638 pages
Book Rating : 4.4/5 (2 download)

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Book Synopsis Computational studies of RNA and DNA by : Jirí Šponer

Download or read book Computational studies of RNA and DNA written by Jirí Šponer and published by Springer Science & Business Media. This book was released on 2006-10-05 with total page 638 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book integrates modern computational studies of nucleic acids, ranging from advanced electronic structure quantum chemical calculations through explicit solvent molecular dynamics (MD) simulations up to mesoscopic modelling, with the main focus given to the MD field. It gives an equal emphasis to the leading methods and applications while successes as well as pitfalls of the computational techniques are discussed.

Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes

Author : Adam Liwo
Publisher : Springer
ISBN 13 : 3319958437
Total Pages : 851 pages
Book Rating : 4.3/5 (199 download)

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Book Synopsis Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes by : Adam Liwo

Download or read book Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes written by Adam Liwo and published by Springer. This book was released on 2018-12-19 with total page 851 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book provides a comprehensive overview of modern computer-based techniques for analyzing the structure, properties and dynamics of biomolecules and biomolecular processes. It is organized in four main parts; the first one deals with methodology of molecular simulations; the second one with applications of molecular simulations; the third one introduces bioinformatics methods and the use of experimental information in molecular simulations; the last part reports on selected applications of molecular quantum mechanics. This second edition has been thoroughly revised and updated to include the latest progresses made in the respective field of research.

RNA 3D Structure Analysis and Prediction

Author : Neocles Leontis
Publisher : Springer Science & Business Media
ISBN 13 : 3642257402
Total Pages : 402 pages
Book Rating : 4.6/5 (422 download)

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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 and Dynamics

Author : Jienyu Ding
Publisher : Springer Nature
ISBN 13 : 1071626876
Total Pages : 256 pages
Book Rating : 4.0/5 (716 download)

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Book Synopsis RNA Structure and Dynamics by : Jienyu Ding

Download or read book RNA Structure and Dynamics written by Jienyu Ding and published by Springer Nature. This book was released on 2022-10-13 with total page 256 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume provides a wide spectrum of multidisciplinary approaches for studying RNA structure and dynamics, including detailed accounts of experimental and computational procedures. Chapters guide readers through cryo-electron microscopy, crystallography, isothermal titration calorimetry, small angle X-ray scattering, single-molecule Förster Energy transfer, X-ray free electron laser, atomic force microscopy, computational simulation, and prediction. Written in the format of the highly successful Methods in Molecular Biology series, each chapter includes an introduction to the topic, lists necessary materials and reagents, includes tips on troubleshooting and known pitfalls, and step-by-step, readily reproducible protocols. Authoritative and cutting-edge, RNA Structure and Dynamics aims to be a foundation for future studies and to be a source of inspiration for new investigations in the field.

Structure and Dynamics of RNA

Author :
Publisher :
ISBN 13 : 9781468451740
Total Pages : 352 pages
Book Rating : 4.4/5 (517 download)

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Book Synopsis Structure and Dynamics of RNA by :

Download or read book Structure and Dynamics of RNA written by and published by . This book was released on 1986-10-31 with total page 352 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Structure and Dynamics of RNA

Author : P. H. van Knippenberg
Publisher : Springer Science & Business Media
ISBN 13 : 1468451731
Total Pages : 335 pages
Book Rating : 4.4/5 (684 download)

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Book Synopsis Structure and Dynamics of RNA by : P. H. van Knippenberg

Download or read book Structure and Dynamics of RNA written by P. H. van Knippenberg and published by Springer Science & Business Media. This book was released on 2013-03-08 with total page 335 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume contains contributions from the speakers at the NATO Advanced Research Workshop on "3D 5tructure and Dynamics of RNA", which was held in Renesse, The Netherlands, 21 - 24 August, 1985. Two major developments have determined the progress of nucleic acid research during the last decade. First, manipulation of genetic material by recombinant DNA methodology has enabled detailed studies of the function of nucleic acids in vivo. 5econd, the use of powerful physical methods, such as X-ray diffraction and nuclear magnetic resonance spectroscopy, in the study of biomacromolecules has provided information regarding the structure and the dynamics of nucleic acids. Both developments were enabled by the advance of synthetic methods that allow preparation of nucleic acid molecules of required sequence and length. The basic understanding of nucleic acid function will ultimately depend on a close collaboration between molecular biologists and biophy sicists. In the case of RNA, the ground rules for the formation of secondary structure have been derived from physical studies of oligoribonucleotides. Powerfull spectroscopic techniques have revealed more details of ~~A structure including novel conformations (e.g. left-handed Z-RNA). A wealth of information has been obtained by studying the relatively small transfer RNA molecules. A few of these RNAs have been crystallized, enabling determination of their three-dimensional structure. It has become apparent that "non-classical" basepairing between distal nucleotides gives rise to tertiary interactions, determining the overall shape of the molecule.

Optimization-based Molecular Dynamics Studies of SARS-CoV-2 Molecular Structures

Author : Jiapu Zhang
Publisher : Springer Nature
ISBN 13 : 3031367731
Total Pages : 956 pages
Book Rating : 4.0/5 (313 download)

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Book Synopsis Optimization-based Molecular Dynamics Studies of SARS-CoV-2 Molecular Structures by : Jiapu Zhang

Download or read book Optimization-based Molecular Dynamics Studies of SARS-CoV-2 Molecular Structures written by Jiapu Zhang and published by Springer Nature. This book was released on 2023-10-16 with total page 956 pages. Available in PDF, EPUB and Kindle. Book excerpt: COVID-19 has brought us extensive research databases in the fields of biophysics, biology, and bioinformatics. To extract valuable structural bioinformatic information of SARS-CoV-2 structural and nonstructural proteins, it is necessary to work with large-scale datasets of molecular dynamics (MD) trajectories that need to be optimized. This monograph serves as a comprehensive guide to optimization-based MD studies of the molecular structures of SARS-CoV-2 proteins and RNA. The book begins by performing local optimization, taking into account the three-body movement and optimizing the noncovalent bonds of each molecular structure. The optimized structures reach a transition state that offers the best stability and lowest energy. The optimization process utilizes a hybrid strategy that combines mathematical optimization with various local search algorithms. This approach significantly reduces data volume while eliminating irrelevant bioinformatics data. To gain a thorough understanding of molecular stability and the mechanism of action, it is essential to consider not only static NMR, X-ray, or cryo-EM structures but also dynamic information obtained through MD or Quantum Mechanics/Molecular Mechanics (QM/MM) simulations. These simulations capture the internal motions and dynamic processes of molecules. Furthermore, for each protein, the structural bioinformatics obtained from the optimized structure is validated by analyzing large-scale MD trajectory databases, which are openly and freely available online. The analysis includes key structural bioinformatics aspects such as salt bridge electrostatic interactions, hydrogen bonds, van der Waals interactions, and hydrophobic interactions specific to each SARS-CoV-2 molecular structure. The book also delves into discussions on drugs, vaccines, and the origins of the virus. Additionally, pandemic mathematical models, including those incorporating time delays, are explored. This book is particularly valuable for professionals working in practical computing roles within computational biochemistry, computational biophysics, optimization and molecular dynamics, structural bioinformatics, biological mathematics, and related fields. It serves as an accessible introduction to these disciplines and is also an excellent teaching resource for students.

Innovations in Biomolecular Modeling and Simulations

Author : Tamar Schlick
Publisher : Royal Society of Chemistry
ISBN 13 : 1849735050
Total Pages : 355 pages
Book Rating : 4.8/5 (497 download)

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Book Synopsis Innovations in Biomolecular Modeling and Simulations by : Tamar Schlick

Download or read book Innovations in Biomolecular Modeling and Simulations written by Tamar Schlick and published by Royal Society of Chemistry. This book was released on 2012-05-24 with total page 355 pages. Available in PDF, EPUB and Kindle. Book excerpt: The chemical and biological sciences face unprecedented opportunities in the 21st century. A confluence of factors from parallel universes - advances in experimental techniques in biomolecular structure determination, progress in theoretical modeling and simulation for large biological systems, and breakthroughs in computer technology - has opened new avenues of opportunity as never before. Now, experimental data can be interpreted and further analysed by modeling, and predictions from any approach can be tested and advanced through companion methodologies and technologies. This two volume set describes innovations in biomolecular modeling and simulation, in both the algorithmic and application fronts. With contributions from experts in the field, the books describe progress and innovation in areas including: simulation algorithms for dynamics and enhanced configurational sampling, force field development, implicit solvation models, coarse-grained models, quantum-mechanical simulations, protein folding, DNA polymerase mechanisms, nucleic acid complexes and simulations, RNA structure analysis and design and other important topics in structural biology modeling. The books are aimed at graduate students and experts in structural biology and chemistry and the emphasis is on reporting innovative new approaches rather than providing comprehensive reviews on each subject.

Biophysical approaches to translational control of gene expression

Author : Jonathan D. Dinman
Publisher : Springer Science & Business Media
ISBN 13 : 1461439914
Total Pages : 325 pages
Book Rating : 4.4/5 (614 download)

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Book Synopsis Biophysical approaches to translational control of gene expression by : Jonathan D. Dinman

Download or read book Biophysical approaches to translational control of gene expression written by Jonathan D. Dinman and published by Springer Science & Business Media. This book was released on 2012-09-20 with total page 325 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book provides a premier resource on understanding the ribosome's essential nature and how it interacts with other proteins and nucleic acids to control protein synthesis. As one of the central foundations in our understanding of the biology at the molecular level, this topic appeals to a wide audience, from bench researcher to clinician. With the advent of atomic scale structures, methods to visualize and separate individual molecules, and the computational power to model the complex interactions of over a million atoms at once, our understanding of how gene expression is controlled at the level of protein translation is now deeply ensconced in the biophysical realm.

Influence of Na+ and Mg2+ Ions on RNA Structures Studied with Molecular Dynamics Simulations

Author : Nina M. Fischer
Publisher :
ISBN 13 :
Total Pages : pages
Book Rating : 4.:/5 (15 download)

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Book Synopsis Influence of Na+ and Mg2+ Ions on RNA Structures Studied with Molecular Dynamics Simulations by : Nina M. Fischer

Download or read book Influence of Na+ and Mg2+ Ions on RNA Structures Studied with Molecular Dynamics Simulations written by Nina M. Fischer and published by . This book was released on 2018 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:

RNA Worlds

Author : John F. Atkins
Publisher :
ISBN 13 : 9780879699468
Total Pages : 0 pages
Book Rating : 4.6/5 (994 download)

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Book Synopsis RNA Worlds by : John F. Atkins

Download or read book RNA Worlds written by John F. Atkins and published by . This book was released on 2011 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume reviews our understanding of two RNA worlds: the primordial RNA world before DNA, in which RNA was both information store and biocatalyst; and the contemporary RNA world, in which mRNA, tRNA, rRNA, siRNA, miRNA, and a host of other RNAs operate.

Innovations in Biomolecular Modeling and Simulations

Author : Tamar Schlick
Publisher : Royal Society of Chemistry
ISBN 13 : 1849735042
Total Pages : 381 pages
Book Rating : 4.8/5 (497 download)

DOWNLOAD NOW!

Book Synopsis Innovations in Biomolecular Modeling and Simulations by : Tamar Schlick

Download or read book Innovations in Biomolecular Modeling and Simulations written by Tamar Schlick and published by Royal Society of Chemistry. This book was released on 2012-05-24 with total page 381 pages. Available in PDF, EPUB and Kindle. Book excerpt: The chemical and biological sciences face unprecedented opportunities in the 21st century. A confluence of factors from parallel universes - advances in experimental techniques in biomolecular structure determination, progress in theoretical modeling and simulation for large biological systems, and breakthroughs in computer technology - has opened new avenues of opportunity as never before. Now, experimental data can be interpreted and further analysed by modeling, and predictions from any approach can be tested and advanced through companion methodologies and technologies. This two volume set describes innovations in biomolecular modeling and simulation, in both the algorithmic and application fronts. With contributions from experts in the field, the books describe progress and innovation in areas including: simulation algorithms for dynamics and enhanced configurational sampling, force field development, implicit solvation models, coarse-grained models, quantum-mechanical simulations, protein folding, DNA polymerase mechanisms, nucleic acid complexes and simulations, RNA structure analysis and design and other important topics in structural biology modeling. The books are aimed at graduate students and experts in structural biology and chemistry and the emphasis is on reporting innovative new approaches rather than providing comprehensive reviews on each subject.

Research Awards Index

Author :
Publisher :
ISBN 13 :
Total Pages : 874 pages
Book Rating : 4.3/5 (91 download)

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Book Synopsis Research Awards Index by :

Download or read book Research Awards Index written by and published by . This book was released on 1988 with total page 874 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Chemistry and Biology of Non-canonical Nucleic Acids

Author : Naoki Sugimoto
Publisher : John Wiley & Sons
ISBN 13 : 3527817883
Total Pages : 288 pages
Book Rating : 4.5/5 (278 download)

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Book Synopsis Chemistry and Biology of Non-canonical Nucleic Acids by : Naoki Sugimoto

Download or read book Chemistry and Biology of Non-canonical Nucleic Acids written by Naoki Sugimoto and published by John Wiley & Sons. This book was released on 2021-03-16 with total page 288 pages. Available in PDF, EPUB and Kindle. Book excerpt: Discover the fundamentals and intricacies of a subject at the interface of chemistry and biology with this authoritative resource Chemistry and Biology of Non-canonical Nucleic Acids delivers a comprehensive treatment of the chemistry and biology of non-canonical nucleic acids, including their history, structures, stabilities, properties, and functions. You'll learn about the role of these vital compounds in transcription, translation, regulation, telomeres, helicases, cancers, neurodegenerative diseases, therapeutic applications, nanotechnology, and more. An ideal resource for graduate students, researchers in physical, organic, analytical, and inorganic chemistry will learn about uncommon nucleic acids, become the common non-canonical nucleic acids that fascinate and engage academics and professionals in private industry. Split into 15 chapters covering a wide range of aspects of non-canonical nucleic acids, the book explains why these compounds exist at the forefront of a new research revolution at the intersection of chemistry and biology. Chemistry and Biology of Non-canonical Nucleic Acids also covers a broad range of topics critical to understanding these versatile and omnipresent chemicals, including: * A discussion of the dynamic regulation of biosystems by nucleic acids with non-canonical structures * The role played by nucleic acid structures in neurodegenerative diseases and various cancers * An exploration of the future outlook for the chemistry and biology of non-canonical nucleic acids * An introduction to the history of canonical and non-canonical structures of nucleic acids * An analysis of the physicochemical properties of non-canonical nucleic acids Perfect for biochemists, materials scientists, and bioengineers, Chemistry and Biology of Non-canonical Nucleic Acids will also earn a place in the libraries of medicinal and pharmaceutical chemists who wish to improve their understanding of life processes and the role that non-canonical nucleic acids play in them.

Computational Structural Biology

Author : Torsten Schwede
Publisher : World Scientific
ISBN 13 : 9812778780
Total Pages : 790 pages
Book Rating : 4.8/5 (127 download)

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Book Synopsis Computational Structural Biology by : Torsten Schwede

Download or read book Computational Structural Biology written by Torsten Schwede and published by World Scientific. This book was released on 2008 with total page 790 pages. Available in PDF, EPUB and Kindle. Book excerpt: This is a comprehensive introduction to Landau-Lifshitz equations and Landau-Lifshitz-Maxwell equations, beginning with the work by Yulin Zhou and Boling Guo in the early 1980s and including most of the work done by this Chinese group led by Zhou and Guo since. The book focuses on aspects such as the existence of weak solutions in multi dimensions, existence and uniqueness of smooth solutions in one dimension, relations with harmonic map heat flows, partial regularity and long time behaviors. The book is a valuable reference book for those who are interested in partial differential equations, geometric analysis and mathematical physics. It may also be used as an advanced textbook by graduate students in these fields.

Molecular Modeling and Simulation

Author : Tamar Schlick
Publisher : Springer Science & Business Media
ISBN 13 : 0387224645
Total Pages : 669 pages
Book Rating : 4.3/5 (872 download)

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Book Synopsis Molecular Modeling and Simulation by : Tamar Schlick

Download or read book Molecular Modeling and Simulation written by Tamar Schlick and published by Springer Science & Business Media. This book was released on 2013-04-18 with total page 669 pages. Available in PDF, EPUB and Kindle. Book excerpt: Very broad overview of the field intended for an interdisciplinary audience; Lively discussion of current challenges written in a colloquial style; Author is a rising star in this discipline; Suitably accessible for beginners and suitably rigorous for experts; Features extensive four-color illustrations; Appendices featuring homework assignments and reading lists complement the material in the main text