ArticleMethods in molecular biology (Clifton, N.J.)2023
RNA 3D Structure Comparison Using RNA-Puzzles Toolkit.
Article in Methods in molecular biology (Clifton, N.J.), 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
What it found
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Who cites it
4 citing papers in PubMed.
- Article
- The RNA-Puzzles Assessments of RNA-Only Targets in CASP16.Proteins · 2026Article
- RNA-Puzzles Round V: blind predictions of 23 RNA structures.Nature methods · 2025Article
- In silico methods for predicting functional synonymous variants.Genome biology · 2023Review
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2 authors.
Funding
Abstract
Computational modeling of RNA three-dimensional (3D) structure may help in unrevealing the molecular mechanisms of RNA molecules and in designing molecules with novel functions. An unbiased blind assessment to benchmark the computational modeling is required to understand the achievements and bottlenecks of the prediction, while a standard structure comparison protocol is necessary. RNA-Puzzles is a community-wide effort on the assessment of blind prediction of RNA tertiary structures. And RNA-Puzzles toolkit is a computational resource derived from RNA-Puzzles, which includes (i) decoy sets generated by different RNA 3D structure prediction methods; (ii) 3D structure normalization, analysis, manipulation, and visualization tools; and (iii) 3D structure comparison metric tools. In this chapter, we illustrate a standard RNA 3D structure prediction assessment protocol using the selected tools from RNA-Puzzles toolkit: rna-tools and RNA_assessment.
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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.