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Investigation Of The Structure And Dynamics Of Rna Systems By Molecular Dynamics Simulations
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Book Synopsis Investigation of the Structure and Dynamics of RNA Systems by Molecular Dynamics Simulations by : Elisabeth Catherina Widjajakusuma
Download or read book Investigation of the Structure and Dynamics of RNA Systems by Molecular Dynamics Simulations written by Elisabeth Catherina Widjajakusuma and published by . This book was released on 2007 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt:
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.
Author :P. H. van Knippenberg Publisher :Springer Science & Business Media ISBN 13 :1468451731 Total Pages :335 pages Book Rating :4.4/5 (684 download)
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.
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.
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:
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.
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.
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.
Book Synopsis Modelling Molecular Structure and Reactivity in Biological Systems by : Kevin Naidoo
Download or read book Modelling Molecular Structure and Reactivity in Biological Systems written by Kevin Naidoo and published by Royal Society of Chemistry. This book was released on 2007-10-31 with total page 305 pages. Available in PDF, EPUB and Kindle. Book excerpt: Computational and theoretical tools for understanding biological processes at the molecular level is an exciting and innovative area of science. Using these methods to study the structure, dynamics and reactivity of biomacromolecules in solution, computational chemistry is becoming an essential tool, complementing the more traditional methods for structure and reactivity determination. Modelling Molecular Structure and Reactivity in Biological Systems covers three main areas in computational chemistry; structure (conformational and electronic), reactivity and design. Initial sections focus on the link between computational and spectroscopic methods in the investigation of electronic structure. The use of Free Energy calculations for the elucidation of reaction mechanisms in enzymatic systems is also discussed. Subsequent sections focus on drug design and the use of database methods to determine ADME (absorption, distribution, metabolism, excretion) properties. This book provides a complete reference on state of the art computational chemistry practised on biological systems. It is ideal for researchers in the field of computational chemistry interested in its application to biological systems.
Book Synopsis Computational Studies of the Structure - Dynamics - Function Relationship by : Dahlia Ruth Weiss
Download or read book Computational Studies of the Structure - Dynamics - Function Relationship written by Dahlia Ruth Weiss and published by . This book was released on 2008 with total page 302 pages. Available in PDF, EPUB and Kindle. Book excerpt:
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.
Book Synopsis Investigation of the Structure and Dynamics of Biologically Relevant RNAs by : Marta L. Zumwalt
Download or read book Investigation of the Structure and Dynamics of Biologically Relevant RNAs written by Marta L. Zumwalt and published by . This book was released on 2006 with total page 230 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Nonlinear Dynamics in Biological Systems by : Jorge Carballido-Landeira
Download or read book Nonlinear Dynamics in Biological Systems written by Jorge Carballido-Landeira and published by Springer. This book was released on 2016-07-20 with total page 134 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book presents recent research results relating to applications of nonlinear dynamics, focusing specifically on four topics of wide interest: heart dynamics, DNA/RNA, cell mobility, and proteins. The book derives from the First BCAM Workshop on Nonlinear Dynamics in Biological Systems, held in June 2014 at the Basque Center of Applied Mathematics (BCAM). At this international meeting, researchers from different but complementary backgrounds, including molecular dynamics, physical chemistry, bio-informatics and biophysics, presented their most recent results and discussed the future direction of their studies using theoretical, mathematical modeling and experimental approaches. Such was the level of interest stimulated that the decision was taken to produce this publication, with the organizers of the event acting as editors. All of the contributing authors are researchers working on diverse biological problems that can be approached using nonlinear dynamics. The book will appeal especially to applied mathematicians, biophysicists, and computational biologists.
Book Synopsis Molecular Dynamics Simulations of Noncanonical Nucleic Acid Structures by : Ty Curtis
Download or read book Molecular Dynamics Simulations of Noncanonical Nucleic Acid Structures written by Ty Curtis and published by . This book was released on 2005 with total page 172 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Experimental and Modelling Investigation of the Dynamics of an RNA Translational Operator by : Jonathan James Westwood
Download or read book Experimental and Modelling Investigation of the Dynamics of an RNA Translational Operator written by Jonathan James Westwood and published by . This book was released on 2010 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: This work focuses on the replicase translational operator (TR) stem loop of the RNA MS2 bacteriophage. Single stranded RNA (ss RNA) viruses are important organisms as they represent pathogenic species in all walks of life including a number of clinically important species such as HIV, Marburg Virus and Ebola. MS2 provides a great model system in which to study regulatory pathways affected by RNA folds due to the extensive biochemical and structural data available. In MS2 the TR stem loop acts as an allosteric switch, via a sequence specific recognition event involving the phage coat protein. Binding of the coat protein dimer to TR signals a switch in the life cycle of the phage from replication to assembly and release. Binding of the coat protein dimer leads to translational repression the viral replicase cistron and also leads to an allosteric conformational change in the protein. TR also contains the AUG start codon for replicase gene and thus is involved in the regulatory pathway of the cistron. Thus any insight to how the folds in the RNA effect binding or translational repression are important for understanding the MS2 virus and other ssRNA viruses like it. The folding ensembles present in solution for a series of RNA oligonucleotides that encompass TR have been examined. Single molecule fluorescence assays suggest that these RNAs exist in solution as differentially base paired/stacked states at equilibrium. What emerges from the experimental is data consistent with an unfolding mechanism in which interruptions to the A- form duplex such as the single stranded loop, the free ends and bulged base of TR, act as nucleation points of unfolding. Additionally substitution of a uracil to a cytosine in the loop causes heterogeneity in the folded and unfolded ensembles relative to the wild-type molecule. This data is used to study folding of the RNAs by 'steered' molecular dynamics (MD) simulations. These show remarkable agreement with experimental data and provide atomistic detail on the molecular interactions which take place during the unfolding pathways studied. The adopted conformers for each simulation provide details about hydrogen bonding between the base pairs of the stem and confirm predicted conformers from apparent dye separation in FRET experiments.
Book Synopsis Advance in Structural Bioinformatics by : Dongqing Wei
Download or read book Advance in Structural Bioinformatics written by Dongqing Wei and published by Springer. This book was released on 2014-11-11 with total page 380 pages. Available in PDF, EPUB and Kindle. Book excerpt: This text examines in detail mathematical and physical modeling, computational methods and systems for obtaining and analyzing biological structures, using pioneering research cases as examples. As such, it emphasizes programming and problem-solving skills. It provides information on structure bioinformatics at various levels, with individual chapters covering introductory to advanced aspects, from fundamental methods and guidelines on acquiring and analyzing genomics and proteomics sequences, the structures of protein, DNA and RNA, to the basics of physical simulations and methods for conformation searches. This book will be of immense value to researchers and students in the fields of bioinformatics, computational biology and chemistry. Dr. Dongqing Wei is a Professor at the Department of Bioinformatics and Biostatistics, College of Life Science and Biotechnology, Shanghai Jiaotong University, Shanghai, China. His research interest is in the general area of structural bioinformatics.
Book Synopsis Structure and Thermodynamics of RNA-protein Interactions by : Carolina Moises Reyes
Download or read book Structure and Thermodynamics of RNA-protein Interactions written by Carolina Moises Reyes and published by . This book was released on 2000 with total page 446 pages. Available in PDF, EPUB and Kindle. Book excerpt:
