Molecular Dynamics Simulations of RNA Systems (Englisch)
- Neue Suche nach: Auffinger, Pascal
- Neue Suche nach: Hartmann, Roland K.
- Neue Suche nach: Bindereif, Albrecht
- Neue Suche nach: Schön, Astrid
- Neue Suche nach: Westhof, Eric
- Neue Suche nach: Auffinger, Pascal
In:
Handbook of RNA Biochemistry
: Second, Completely Revised and Enlarged Edition
;
687-718
;
2014
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ISBN:
- Aufsatz/Kapitel (Buch) / Elektronische Ressource
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Titel:Molecular Dynamics Simulations of RNA Systems
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Beteiligte:Hartmann, Roland K. ( Herausgeber:in ) / Bindereif, Albrecht ( Herausgeber:in ) / Schön, Astrid ( Herausgeber:in ) / Westhof, Eric ( Herausgeber:in ) / Auffinger, Pascal ( Autor:in )
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Erschienen in:Handbook of RNA Biochemistry : Second, Completely Revised and Enlarged Edition ; 687-718
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Verlag:
- Neue Suche nach: Wiley‐VCH Verlag GmbH & Co. KGaA
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Erscheinungsort:Weinheim, Germany
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Erscheinungsdatum:09.04.2014
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Format / Umfang:31 pages
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ISBN:
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DOI:
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Medientyp:Aufsatz/Kapitel (Buch)
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Format:Elektronische Ressource
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Sprache:Englisch
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Schlagwörter:parameterization , X‐ray structures , DNA , conformational transitions , equilibration procedures , (rare) non‐covalent interactions , adding hydrogen atoms , selection of starting structure , liquid phase , protonation , solvent analysis , time scale of simulation , Molecular dynamics (MD) , biomolecular systems , hydration , multiple molecular dynamics (MMD) , ion‐binding sites , stability and quality of trajectories , divalent ions , nucleic acids , water molecules , force fields , RNA , simulations , electrostatic interactions , crystal phase , simulation protocols , ligands , conformational check , monovalent ions , thermodynamic ensemble , solvation , clustering artifacts
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Datenquelle:
Inhaltsverzeichnis E-Book
Die Inhaltsverzeichnisse werden automatisch erzeugt und basieren auf den im Index des TIB-Portals verfügbaren Einzelnachweisen der enthaltenen Beiträge. Die Anzeige der Inhaltsverzeichnisse kann daher unvollständig oder lückenhaft sein.
- 1
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Enzymatic RNA Synthesis Using Bacteriophage T7 RNA PolymeraseGößringer, Markus / Helmecke, Dominik / Köhler, Karen / Schön, Astrid / Kirsebom, Leif A. / Bindereif, Albrecht / Hartmann, Roland K. et al. | 2014
- 29
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Production of RNAs with Homogeneous 5′‐ and 3′‐EndsMörl, Mario / Hartmann, Roland K. et al. | 2014
- 45
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RNA LigationTurunen, Janne J. / Pavlova, Liudmila V. / Hengesbach, Martin / Helm, Mark / Müller, Sabine / Hartmann, Roland K. / Frilander, Mikko J. et al. | 2014
- 89
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Northern Blot Detection of Small RNAsBeckmann, Benedikt M. / Grünweller, Arnold / Hartmann, Roland K. et al. | 2014
- 105
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Rapid, Non‐Denaturing, Large‐Scale Purification of In Vitro Transcribed RNA Using Weak Anion‐Exchange ChromatographyEaston, Laura E. / Shibata, Yoko / Lukavsky, Peter J. et al. | 2014
- 117
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3′‐Terminal Attachment of Fluorescent Dyes and BiotinWillkomm, Dagmar K. / Hartmann, Roland K. et al. | 2014
- 129
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Chemical RNA Synthesis, Purification, and AnalysisSproat, Brian S. et al. | 2014
- 151
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Modified RNAs as Tools in RNA BiochemistryEdwards, Thomas E. / Sigurdsson, Snorri Th. et al. | 2014
- 173
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Direct Determination of RNA Sequence and Modification by Radiolabeling MethodsGimple, Olaf / Schön, Astrid et al. | 2014
- 205
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Probing RNA Structure In Vitro with Enzymes and ChemicalsHelfer, Anne‐Catherine / Romilly, Cédric / Chevalier, Clément / Lioliou, Efthimia / Marzi, Stefano / Romby, Pascale et al. | 2014
- 231
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Probing RNA Solution Structure by Photocrosslinking: Incorporation of Photoreactive Groups at RNA Termini and Determination of Crosslinked Sites by Primer ExtensionHarris, Michael E. et al. | 2014
- 255
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Terbium(III) Footprinting as a Probe of RNA Structure and Metal Binding SitesHarris, Dinari A. / Todd, Gabrielle C. / Walter, Nils G. et al. | 2014
- 269
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Pb2+‐Induced Cleavage of RNAKirsebom, Leif A. / Ciesiolka, Jerzy et al. | 2014
- 285
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Identification and Characterization of Metal Ion Coordination Interactions with RNA by Quantitative Analysis of Thiophilic Metal Ion Rescue of Site‐Specific Phosphorothioate ModificationsHarris, Michael E. et al. | 2014
- 301
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Probing RNA Structure and Ligand Binding Sites on RNA by Fenton CleavageHeidrich, Corina G. / Berens, Christian et al. | 2014
- 319
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Measuring the Stoichiometry of Magnesium Ions Bound to RNAAndrews, Andrew J. / Fierke, Carol A. et al. | 2014
- 329
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Nucleotide Analog Interference Mapping and Suppression (NAIM/NAIS): a Combinatorial Approach to Study RNA Structure, Folding, and Interaction with ProteinsFedorova, Olga / Boudvillain, Marc / Waldsich, Christina et al. | 2014
- 369
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Nucleotide Analog Interference Mapping (NAIM): Application to the RNase P SystemCuzic‐Feltens, Simona / Hartmann, Roland K. et al. | 2014
- 397
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Identification of Divalent Metal Ion Binding Sites in RNA/DNA‐Metabolizing Enzymes by Fe(II)‐Mediated Hydroxyl Radical CleavageRen, Yan‐Guo / Henriksson, Niklas / Virtanen, Anders et al. | 2014
- 407
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RNA Structure and Folding Analyzed Using Small‐Angle X‐Ray ScatteringBaird, Nathan J. / West, Jeremey / Sosnick, Tobin R. et al. | 2014
- 427
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Temperature‐Gradient Gel Electrophoresis of RNARiesner, Detlev / Steger, Gerhard et al. | 2014
- 445
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UV Melting Studies with RNADumas, Philippe / Ennifar, Eric / Disdier, François / Walter, Philippe et al. | 2014
- 481
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RNA CrystallizationKondo, Jiro / Sauter, Claude / Masquida, Benoît et al. | 2014
- 499
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Studying RNA Using Single Molecule Fluorescence Resonance Energy TransferSpenkuch, Felix / Domingo, Olwen / Hinze, Gerald / Basché, Thomas / Helm, Mark et al. | 2014
- 527
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Atomic Force Microscopy Imaging and Force Spectroscopyof RNABussiek, Malte / Schöne, Antonie / Nellen, Wolfgang et al. | 2014
- 547
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Secondary Structure PredictionSteger, Gerhard et al. | 2014
- 579
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RNA Secondary Structure Analysis Using Abstract ShapesGiegerich, Robert / Voß, Björn et al. | 2014
- 595
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Screening Genome Sequences for known RNA Genes or MotifsGautheret, Daniel et al. | 2014
- 619
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Homology Search for Small Structured Non‐coding RNAsMarz, Manja / Wehner, Stefanie / Stadler, Peter F. et al. | 2014
- 633
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Predict RNA 2D and 3D Structure over the Internet Using MC‐ToolsLeong Koan, Stephen / Roy, Jonathan / Parisien, Marc / Major, François et al. | 2014
- 667
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S2S‐Assemble2: a Semi‐Automatic Bioinformatics Framework to Study and Model RNA 3D ArchitecturesJossinet, Fabrice / Westhof, Eric et al. | 2014
- 687
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Molecular Dynamics Simulations of RNA SystemsAuffinger, Pascal et al. | 2014
- 719
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Identification and Characterization of Small Non‐coding RNAs in BacteriaPodkaminski, Dimitri / Bouvier, Marie / Vogel, Jörg et al. | 2014
- 787
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The Identification of Bacterial Non‐coding RNAs through Complementary ApproachesVoß, Björn / Hess, Wolfgang R. et al. | 2014
- 801
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Experimental RNomics, a Global Approach to Identify Non‐coding RNAs in Model Organisms, and RNPomics to Analyze the Non‐coding RNP TranscriptomeRederstorff, Mathieu / Hüttenhofer, Alexander et al. | 2014
- 821
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Computational Methods for Gene Expression Profiling Using Next‐Generation Sequencing (RNA‐Seq)Castle, John C. et al. | 2014
- 833
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Characterization and Prediction of miRNA TargetsHausser, Jean / Zavolan, Mihaela et al. | 2014
- 861
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Barcoded cDNA Libraries for miRNA Profiling by Next‐Generation SequencingHafner, Markus / Renwick, Neil / Pena, John / Mihailovic, Aleksandra / Tuschl, Thomas et al. | 2014
- 877
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Transcriptome‐Wide Identification of Protein Binding Sites on RNA by PAR‐CLIP (Photoactivatable‐Ribonucleoside‐Enhanced Crosslinking and Immunoprecipitation)Hoell, Jessica I. / Hafner, Markus / Landthaler, Markus / Ascano, Manuel / Farazi, Thalia A. / Wardle, Greg / Nusbaum, Jeff / Cekan, Pavol / Khorshid, Mohsen / Burger, Lukas et al. | 2014
- 899
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Global Analysis of Protein–RNA Interactions with Single‐Nucleotide Resolution Using iCLIPKönig, Julian / McGlincy, Nicholas J. / Ule, Jernej et al. | 2014
- 919
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Use of RNA Affinity Matrices for the Isolation of RNA Binding ProteinsEnglert, Markus / Späth, Bettina / Schiffer, Steffen / Rösch, Sylvia / Beier, Hildburg / Marchfelder, Anita et al. | 2014
- 935
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Biotin‐Based Affinity Purification of RNA–Protein ComplexesPreußner, Marco / Schreiner, Silke / Grishina, Inna / Palfi, Zsofia / Hui, Jingyi / Bindereif, Albrecht et al. | 2014
- 957
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Affinity Purification of Spliceosomal and Small Nuclear Ribonucleoprotein ComplexesDannenberg, Julia / Fabrizio, Patrizia / Will, Cindy L. / Lührmann, Reinhard et al. | 2014
- 975
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Study of RNA–Protein Interactions and RNA Structure in Ribonucleoprotein Particles (RNPs)Marchand, Virginie / Mougin, Annie / Méreau, Agnès / Behm‐Ansmant, Isabelle / Motorin, Yuri / Branlant, Christiane et al. | 2014
- 1017
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Immunopurification of Endogenous RNAs Associated with RNA Binding Proteins In vivoÄnkö, Minna‐Liisa / Neugebauer, Karla M. et al. | 2014
- 1029
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Protein–RNA Crosslinking in Native Ribonucleoprotein ParticlesDybkov, Olexandr / Urlaub, Henning / Lührmann, Reinhard et al. | 2014
- 1055
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Sedimentation Analysis of Ribonucleoprotein ComplexesRösel, Tanja / Medenbach, Jan / Damianov, Andrey / Schreiner, Silke / Bindereif, Albrecht et al. | 2014
- 1067
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Identification and Characterization of RNA Binding Proteins through Three‐Hybrid AnalysisScott, Felicia / Engelke, David R. et al. | 2014
- 1087
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Experimental Identification of MicroRNA TargetsBeitzinger, Michaela / Meister, Gunter et al. | 2014
- 1097
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Aptamer Selection against Biological Macromolecules: Proteins and CarbohydratesPeter, Franziska / Voertler, C. Stefan et al. | 2014
- 1139
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In Vitro Selection against Small TargetsEulberg, Dirk / Maasch, Christian / Purschke, Werner G. / Klussmann, Sven et al. | 2014
- 1165
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SELEX Strategies to Identify Antisense and Protein Target Sites in RNA or hnRNP ComplexesLützelberger, Martin / Jakobsen, Martin R. / Kjems, Jørgen et al. | 2014
- 1185
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Genomic SELEXBoots, Jennifer L. / Matylla‐Kulinska, Katarzyna / Zywicki, Marek / Zimmermann, Bob / Schroeder, Renée et al. | 2014
- 1207
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In vivo SELEX StrategiesCooper, Thomas A. et al. | 2014
- 1221
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Gene Silencing Methods Using Vector‐Encoded siRNAs or miRNAsPoi Liu, Ying / Berkhout, Ben et al. | 2014
- 1243
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Using Chemical Modification to Enhance siRNA PerformanceBramsen, Jesper B. / Grünweller, Arnold / Hartmann, Roland K. / Kjems, Jørgen et al. | 2014
- 1279
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Appendix: UV Spectroscopy for the Quantitation of RNA| 2014
- 1283
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Index| 2014
- I
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Front Matter| 2014