| scholarly article | Q13442814 |
| P50 | author | Jesse Stombaugh | Q110875143 |
| P2093 | author name string | Jiri Sponer | |
| Judit E Sponer | |||
| Craig L Zirbel | |||
| Neocles B Leontis | |||
| P2860 | cites work | Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density | Q21708802 |
| Geometric nomenclature and classification of RNA base pairs | Q24539990 | ||
| The European ribosomal RNA database | Q24600334 | ||
| The RCSB Protein Data Bank: a redesigned query system and relational database based on the mmCIF schema | Q24794858 | ||
| The comparative RNA web (CRW) site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs | Q24802442 | ||
| Molecular dynamics simulations of sarcin-ricin rRNA motif. | Q25255860 | ||
| Structural and evolutionary classification of G/U wobble basepairs in the ribosome | Q25255904 | ||
| Structure of the 30S ribosomal subunit | Q27627261 | ||
| Transition state stabilization by a catalytic RNA | Q27639765 | ||
| A comparison of vanadate to a 2'-5' linkage at the active site of a small ribozyme suggests a role for water in transition-state stabilization | Q27644728 | ||
| Metals, motifs, and recognition in the crystal structure of a 5S rRNA domain | Q27748294 | ||
| Crystal structure of the ribosomal RNA domain essential for binding elongation factors | Q27766007 | ||
| Structure of the 70S ribosome complexed with mRNA and tRNA | Q27860602 | ||
| SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling | Q27860614 | ||
| Structures of the bacterial ribosome at 3.5 A resolution | Q27860848 | ||
| An extended structural signature for the tRNA anticodon loop | Q28364135 | ||
| The building blocks and motifs of RNA architecture | Q29031588 | ||
| FR3D: finding local and composite recurrent structural motifs in RNA 3D structures | Q33724971 | ||
| Evolutionary profiles from the QR factorization of multiple sequence alignments | Q33932608 | ||
| A common motif organizes the structure of multi-helix loops in 16 S and 23 S ribosomal RNAs | Q34067749 | ||
| Non-Watson-Crick basepairing and hydration in RNA motifs: molecular dynamics of 5S rRNA loop E. | Q34181373 | ||
| Structural domains of transfer RNA molecules | Q34321933 | ||
| Electronic properties, hydrogen bonding, stacking, and cation binding of DNA and RNA bases | Q34561384 | ||
| Analysis of RNA motifs | Q35165221 | ||
| A guide to ions and RNA structure | Q35670060 | ||
| The UA_handle: a versatile submotif in stable RNA architectures | Q37041795 | ||
| Molecular dynamics suggest multifunctionality of an adenine imino group in acid-base catalysis of the hairpin ribozyme. | Q37142097 | ||
| Nature and magnitude of aromatic stacking of nucleic acid bases | Q37157535 | ||
| Frequency and isostericity of RNA base pairs | Q37169773 | ||
| Sugar edge/sugar edge base pairs in RNA: stabilities and structures from quantum chemical calculations | Q40305810 | ||
| GNRA tetraloops make a U-turn | Q43117755 | ||
| Proton exchange and base-pair kinetics of poly(rA).poly(rU) and poly(rI).poly(rC). | Q44019922 | ||
| The roles of ribosomal proteins in the structure assembly, and evolution of the large ribosomal subunit | Q44926888 | ||
| Anion binding to nucleic acids | Q47964522 | ||
| Motif prediction in ribosomal RNAs Lessons and prospects for automated motif prediction in homologous RNA molecules | Q48271573 | ||
| Leading RNA tertiary interactions: structures, energies, and water insertion of A-minor and P-interactions. A quantum chemical view. | Q51911482 | ||
| Energies, structures, and electronic properties of molecules in solution with the C-PCM solvation model. | Q52019488 | ||
| Accurate Interaction Energies of Hydrogen-Bonded Nucleic Acid Base Pairs | Q58445500 | ||
| Structure, Energetics, and Dynamics of the Nucleic Acid Base Pairs: NonempiricalAb InitioCalculations | Q58445773 | ||
| Theoretical Methods for the Description of the Solvent Effect in Biomolecular Systems | Q62141691 | ||
| Rapid chemical probing of conformation in 16 S ribosomal RNA and 30 S ribosomal subunits using primer extension | Q68961173 | ||
| Studies of base pair kinetics by NMR measurement of proton exchange | Q70919655 | ||
| The Mg2+ binding sites of the 5S rRNA loop E motif as investigated by molecular dynamics simulations | Q73599034 | ||
| P433 | issue | 15 | |
| P407 | language of work or name | English | Q1860 |
| P304 | page(s) | 4898-4918 | |
| P577 | publication date | 2009-06-14 | |
| P1433 | published in | Nucleic Acids Research | Q135122 |
| P1476 | title | Classification and energetics of the base-phosphate interactions in RNA | |
| P478 | volume | 37 |
| Q49615824 | A nucleobase-centered coarse-grained representation for structure prediction of RNA motifs. |
| Q41051818 | Accurate prediction of RNA nucleotide interactions with backbone k-tree model |
| Q38660825 | All-Atom MD Predicts Magnesium-Induced Hairpin in Chemically Perturbed RNA Analog of F10 Therapeutic. |
| Q41821468 | An atlas of RNA base pairs involving modified nucleobases with optimal geometries and accurate energies |
| Q89076059 | An intricate balance of hydrogen bonding, ion atmosphere and dynamics facilitates a seamless uracil to cytosine substitution in the U-turn of the neomycin-sensing riboswitch |
| Q38348974 | An introduction to recurrent nucleotide interactions in RNA. |
| Q28649737 | Annotating RNA motifs in sequences and alignments |
| Q42542943 | Building a stable RNA U-turn with a protonated cytidine. |
| Q35899062 | CHSalign: A Web Server That Builds upon Junction-Explorer and RNAJAG for Pairwise Alignment of RNA Secondary Structures with Coaxial Helical Stacking |
| Q41095160 | Chemical feasibility of the general acid/base mechanism of glmS ribozyme self-cleavage |
| Q34509998 | ClaRNA: a classifier of contacts in RNA 3D structures based on a comparative analysis of various classification schemes |
| Q37852524 | Computational approaches to 3D modeling of RNA. |
| Q37868135 | Computational approaches to RNA structure prediction, analysis, and design |
| Q35124317 | Computational model for predicting experimental RNA and DNA nearest-neighbor free energy rankings |
| Q51628984 | Computer Folding of RNA Tetraloops: Identification of Key Force Field Deficiencies. |
| Q30584761 | Conformational dynamics of the human propeller telomeric DNA quadruplex on a microsecond time scale. |
| Q35182668 | Correlating SHAPE signatures with three-dimensional RNA structures |
| Q92944514 | Estimating Strengths of Individual Hydrogen Bonds in RNA Base Pairs: Toward a Consensus between Different Computational Approaches |
| Q40623105 | Extensive molecular dynamics simulations showing that canonical G8 and protonated A38H+ forms are most consistent with crystal structures of hairpin ribozyme |
| Q37021669 | Free-energy landscape of a hyperstable RNA tetraloop |
| Q30402159 | Fully differentiable coarse-grained and all-atom knowledge-based potentials for RNA structure evaluation |
| Q41892822 | Higher order structural effects stabilizing the reverse Watson-Crick Guanine-Cytosine base pair in functional RNAs. |
| Q59125461 | How to fold and protect mitochondrial ribosomal RNA with fewer guanines |
| Q38112952 | How to understand quantum chemical computations on DNA and RNA systems? A practical guide for non-specialists |
| Q36002417 | Identifying novel sequence variants of RNA 3D motifs |
| Q37624617 | Isosteric and nonisosteric base pairs in RNA motifs: molecular dynamics and bioinformatics study of the sarcin-ricin internal loop |
| Q60913129 | Molecular basis for the increased affinity of an RNA recognition motif with re-engineered specificity: A molecular dynamics and enhanced sampling simulations study |
| Q34189280 | Molecular dynamics simulations suggest that RNA three-way junctions can act as flexible RNA structural elements in the ribosome |
| Q36158558 | Molecular mechanism for preQ1-II riboswitch function revealed by molecular dynamics |
| Q42062129 | Molecular mechanism of preQ1 riboswitch action: a molecular dynamics study |
| Q42242007 | NMR elucidation of the role of Mg2+ in the structure and stability of the conserved RNA motifs of the EMCV IRES element |
| Q50070051 | NMR experiments for the rapid identification of P=O···H-X type hydrogen bonds in nucleic acids. |
| Q34532960 | Network Theory Tools for RNA Modeling |
| Q53291087 | On the expansion of ribosomal proteins and RNAs in eukaryotes. |
| Q35656731 | On the mechanism of RNA phosphodiester backbone cleavage in the absence of solvent |
| Q33799139 | On the role of Hoogsteen:Hoogsteen interactions in RNA: ab initio investigations of structures and energies |
| Q37760981 | Predicting and modeling RNA architecture |
| Q39354341 | QM/MM studies of hairpin ribozyme self-cleavage suggest the feasibility of multiple competing reaction mechanisms |
| Q28834147 | Quantum chemical studies of nucleic acids: can we construct a bridge to the RNA structural biology and bioinformatics communities? |
| Q36300117 | R3D Align: global pairwise alignment of RNA 3D structures using local superpositions |
| Q35810086 | R3D-2-MSA: the RNA 3D structure-to-multiple sequence alignment server |
| Q47235409 | RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview. |
| Q34041586 | RNA structural motifs that entail hydrogen bonds involving sugar–phosphate backbone atoms of RNA |
| Q41209881 | RNABP COGEST: a resource for investigating functional RNAs |
| Q40414870 | Revisiting GNRA and UNCG folds: U-turns versus Z-turns in RNA hairpin loops. |
| Q35087348 | Sequence dependent variations in RNA duplex are related to non-canonical hydrogen bond interactions in dinucleotide steps. |
| Q34505971 | SimRNA: a coarse-grained method for RNA folding simulations and 3D structure prediction |
| Q48050340 | Simultaneous NMR characterisation of multiple minima in the free energy landscape of an RNA UUCG tetraloop |
| Q29299984 | Stacking in RNA: NMR of Four Tetramers Benchmark Molecular Dynamics |
| Q51283756 | Structural and energetic characterization of the emissive RNA alphabet based on the isothiazolo[4,3-d]pyrimidine heterocycle core. |
| Q42244106 | Structure and mechanical properties of the ribosomal L1 stalk three-way junction. |
| Q47441033 | Tetraloop-like geometries could form the basis of the catalytic activity of the most ancient ribooligonucleotides |
| Q38052698 | The DNA and RNA sugar-phosphate backbone emerges as the key player. An overview of quantum-chemical, structural biology and simulation studies |
| Q53276095 | The Expansion Segments of 28S Ribosomal RNA Extensively Match Human Messenger RNAs. |
| Q37274501 | The GA-minor submotif as a case study of RNA modularity, prediction, and design. |
| Q37661791 | The Nucleic Acid Database: new features and capabilities |
| Q37038739 | The RNA 3D Motif Atlas: Computational methods for extraction, organization and evaluation of RNA motifs |
| Q34058321 | The RNA backbone plays a crucial role in mediating the intrinsic stability of the GpU dinucleotide platform and the GpUpA/GpA miniduplex |
| Q91651443 | The effect of adenine protonation on RNA phosphodiester backbone bond cleavage elucidated by deaza-nucleobase modifications and mass spectrometry |
| Q39744179 | The influence of the local sequence environment on RNA loop structures |
| Q33901748 | Theory and Modeling of RNA Structure and Interactions with Metal Ions and Small Molecules |
| Q36033772 | Understanding the Sequence Preference of Recurrent RNA Building Blocks using Quantum Chemistry: The Intrastrand RNA Dinucleotide Platform |
| Q35075517 | WebFR3D--a server for finding, aligning and analyzing recurrent RNA 3D motifs |
Search more.