ReviewCold Spring Harbor perspectives in biology2011
Predicting and modeling RNA architecture.
Review in Cold Spring Harbor perspectives in biology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
21 citing papers in PubMed.
- Inconsistencies in the Classification of the Family Cydnidae (Hemiptera: Heteroptera: Pentatomoidea) Revealed by Molecular Apomorphies in the Secondary and Tertiary Structures of 18S rRNA Length-Variable Region L (LVR L).International journal of molecular sciences · 2024Article
- Context-dependence of T-loop Mediated Long-range RNA Tertiary Interactions.Journal of molecular biology · 2023Article
- R2DT is a framework for predicting and visualising RNA secondary structure using templates.Nature communications · 2021Article
- Article
- Conformational adaptation of UNCG loops upon crowding.RNA (New York, N.Y.) · 2019Article
- Using Rosetta for RNA homology modeling.Methods in enzymology · 2019Article
- Thermodynamic stabilities of three-way junction nanomotifs in prohead RNA.RNA (New York, N.Y.) · 2017Article
- Incorporation of thio-pseudoisocytosine into triplex-forming peptide nucleic acids for enhanced recognition of RNA duplexes.Nucleic acids research · 2014Article
- RNA structure analysis of human spliceosomes reveals a compact 3D arrangement of snRNAs at the catalytic core.The EMBO journal · 2013Article
- Widespread purifying selection on RNA structure in mammals.Nucleic acids research · 2013Article
- The essential role of stacking adenines in a two-base-pair RNA kissing complex.Journal of the American Chemical Society · 2013Article
- Information-theoretic uncertainty of SCFG-modeled folding space of the non-coding RNA.Journal of theoretical biology · 2013Article
- The RNA worlds in context.Cold Spring Harbor perspectives in biology · 2012Article
- Twins, quadruplexes, and more: functional aspects of native and engineered RNA self-assemblyFrontiers in life science · 2012Article
- RNA modeling, naturally.Proceedings of the National Academy of Sciences of the United States of America · 2012Article
- Modeling and design by hierarchical natural moves.Proceedings of the National Academy of Sciences of the United States of America · 2012Article
- Article
- Site-specific platinum(II) cross-linking in a ribozyme active site.Journal of the American Chemical Society · 2012Article
- Structure and stability of RNA/RNA kissing complex: with application to HIV dimerization initiation signal.RNA (New York, N.Y.) · 2011Article
- NMR structure of a 4 x 4 nucleotide RNA internal loop from an R2 retrotransposon: identification of a three purine-purine sheared pair motif and comparison to MC-SYM predictions.RNA (New York, N.Y.) · 2011Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
A general approach for modeling the architecture of large and structured RNA molecules is described. The method exploits the modularity and the hierarchical folding of RNA architecture that is viewed as the assembly of preformed double-stranded helices defined by Watson-Crick base pairs and RNA modules maintained by non-Watson-Crick base pairs. Despite the extensive molecular neutrality observed in RNA structures, specificity in RNA folding is achieved through global constraints like lengths of helices, coaxiality of helical stacks, and structures adopted at the junctions of helices. The Assemble integrated suite of computer tools allows for sequence and structure analysis as well as interactive modeling by homology or ab initio assembly with possibilities for fitting within electronic density maps. The local key role of non-Watson-Crick pairs guides RNA architecture formation and offers metrics for assessing the accuracy of three-dimensional models in a more useful way than usual root mean square deviation (RMSD) values.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.