Evidence map›Paper›PMID 28730430›Full record

ArticleMethods in molecular biology (Clifton, N.J.)2017

Computational Generation of RNA Nanorings.

Rishabh Sharan, Eckart Bindewald, Wojciech K Kasprzak, Bruce A Shapiro

Abstract read
In one paragraph

Article in Methods in molecular biology (Clifton, N.J.), 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

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.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

2 citing papers in PubMed.

  1. Review
  2. Review
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

4 authors.

Rishabh SharanRNA Structure and Design Section, RNA Biology Laboratory, National Cancer Institute, National Institutes of Health, Frederick, MD, 21702, USA.
Eckart BindewaldFrederick National Laboratory for Cancer Research, Leidos Biomedical Research, Frederick, MD, USA.
Wojciech K KasprzakBasic Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA.
Bruce A ShapiroRNA Structure and Design Section, RNA Biology Laboratory, National Cancer Institute, National Institutes of Health, Frederick, MD, 21702, USA. shapirbr@mail.nih.gov.

Funding

COMPUTER ANALYSIS OF NUCLEIC ACID STRUCTUREZ01BC008382 · NCI · DIVISION OF BASIC SCIENCES - NCI · PI SHAPIRO, BRUCE A. · 1996 to 2008
$1.2M
Computational RNA NanodesignZ01BC011061 · NCI · DIVISION OF BASIC SCIENCES - NCI · PI SHAPIRO, BRUCE · 2008 to 2008
$513k
CCR NIH HHS HHSN261200800001CIntramural NIH HHS Z01 BC008382Intramural NIH HHS Z01 BC011061NCI NIH HHS HHSN261200800001E
6 · The paper itself

Abstract

A variety of designed RNA ring structures (ranging from triangles to hexagonal rings) have been reported in the scientific literature. Designing self-assembling RNA ring structures from structural motifs is, however, a nontrivial problem as there are many combinations of motifs and linking helices. Moreover, most combinations of motifs and linker helices will not lead to ring closure. A solution to this problem was recently published using a "design-by-catalog" approach where motif combinations that lead to rings are precomputed and tabulated. Here we present a web-browser based workflow for creating RNA rings using Galaxy, a web-based platform that can be used for workflow management. An example of how these RNA rings are generated and processed to create a 3D model of the ring is discussed.

Indexed as

Models, MolecularNucleic Acid ConformationComputational BiologyMutationRNASoftwareWeb BrowserRNAClosureEnumerationRingRNAScaffold

Identifiers

PMID28730430
PMCPMC10802920

What OpenQuestion holds

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Registered trials

None linked

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.