Citations in PubMed

Primary Citation PubMed: 12592009 Citations in PubMed

PDB ID Mentions in PubMed Central Article count: 3

Citations in PubMed

This linkout lists citations, indexed by PubMed, to the Primary Citation for this PDB ID.

PDB ID Mentions in PubMed Central

Data mentions are occurrences of PDB IDs in the full text articles from the PubMedCentral Open Access Subset of currently about 1 million articles. For each article, the sentences containing the PDB ID are listed. Article titles can be filtered by keywords and sorted by year.

  • 3 per page
  • 5 per page
  • 10 per page
  • view all
  • Publication Year
  • Ascending
  • Descending

A novel cGUUAg tetraloop structure with a conserved yYNMGg-type backbone conformation from cloverleaf 1 of bovine enterovirus 1 RNA.

(2005) Nucleic Acids Res 33

PubMed: 15814817 | PubMedCentral: PMC1074726 | DOI: 10.1093/nar/gki501

The backbone conformation and the base-stacking pattern of the cGUUAg-loop, however, are highly similar to that of the coxsackieviral uCACGg D-loop (PDB 1RFR) and of the stable cUUCGg tetraloop (PDB 1... 7Y) but surprisingly dissimilar to the structure of a cGUAAg stable tetraloop (PDB 1MSY), even though the cGU U Ag BEV D-loop and the cGU A Ag tetraloop differ by 1 nt only.

( D ) Superimposition (backbone atoms of loop and closing base pair, top view) of the apical loop region of the BEVSLDap structure (nt 61–66, red) with the crystal structure of the cGUAAg tetraloop (blue, PDB 1MSY).

Publication Year: 2005


The RNA backbone plays a crucial role in mediating the intrinsic stability of the GpU dinucleotide platform and the GpUpA/GpA miniduplex.

(2010) Nucleic Acids Res 38

PubMed: 20223772 | PubMedCentral: PMC2919703 | DOI: 10.1093/nar/gkq155

The structural fragment shown here is taken from PDB entry 1MSY ( 6 ).

The structures shown in A and B depict the G 2655 pU 2656 platform from a 27-nt fragment that mimics the sarcin/ricin loop from E. coli 23S rRNA [PDB entry 1MSY ( 6 )].

Publication Year: 2010


PubMed ID is not available.

Published in 2015

PubMedCentral: PMC4446410

Comparison of performance of distance-dependent energy, dihedral-dependent energy, and total energy of 3dRNAscore in test set II Decoy RNA Length Method Enrichment score (DI) Distance term Dihedral te... m Total Position restrained dynamics and REMD (A) 1duq 26 X-ray 8.2 7.5 8.3 1f27 30 X-ray 7.9 5.7 8.1 1msy 27 X-ray 7.4 6.7 7.6 1nuj 24 X-ray 7.3 7.5 7.4 434d 14 X-ray 7.5 7.0 7.6 Normal modes (B) 1duq 26 X-ray 6.3 4.8 6.9 1esy 19 NMR 6.5 5.2 6.5 1f27 30 X-ray 6.7 4.3 6.7 1i9v 76 X-ray 5.5 4.6 5.5 1kka 17 NMR 6.9 2.6 6.9 1msy 27 X-ray 6.3 4.7 6.7 1nuj 24 X-ray 4.5 1.6 4.5 1qwa 21 NMR 3.5 2.2 3.7 1×9k 62 X-ray 3.1 2.5 3.1 1xjr 46 X-ray 5.8 4.8 6.2 1ykq 19 X-ray 5.2 5.0 5.0 1zih 12 NMR 5.9 3.4 6.9 28sp 28 NMR 6.1 5.4 5.7 2f88 34 NMR 3.9 3.2 4.1 434d 14 X-ray 6.5 5.2 6.9 FARNA (C) 1a4d 41 NMR 1.8 2.4 2.1 1csl 28 X-ray 2.2 1.8 2.4 1dqf 19 X-ray 3.6 2.0 3.6 1esy 19 NMR 3.8 2.4 3.8 1i9x 26 X-ray 4.2 1.6 4.0 1j6s 24 X-ray 0.6 2.2 1.6 1kd5 22 X-ray 2.4 1.6 2.4 1kka 17 NMR 1.7 0.8 2.0 1l2x 27 X-ray 0.4 1.4 1.5 1mhk 32 X-ray 1.2 0.6 1.4 1q9a 27 X-ray 3.0 1.6 3.2 1qwa 21 NMR 1.2 0.6 1.4 1xjr 46 X-ray 3.0 1.8 3.2 1zih 12 NMR 6.8 2.4 6.8 255d 24 X-ray 1.8 0.8 2.0 283d 24 X-ray 1.7 0.6 1.8 28sp 28 NMR 3.6 4.2 3.8 2a43 26 X-ray 2.8 1.4 3.2 2f88 34 NMR 3.5 2.1 3.6 Average values (A) 7.66 6.88 7.80 (B) 5.51 3.97 5.69 (C) 2.59 1.70 2.83 X-ray 4.43 3.43 4.65 NMR 4.25 2.84 4.41 All 4.37 3.24 4.57 Table 4.

Comparison of the performance of 3dRNAscore, KB potential and Rosetta methods in test set II Decoy RNA Length Method Enrichment score (RMSD) Enrichment score (DI) 3dRNAscore KB RASP Rosetta 3dRNAscore KB RASP Rosetta Position restrained dynamics and REMD (A) 1duq 26 X-ray 8.5 7.6 7.6 7.1 8.3 7.5 7.6 7.0 1f27 30 X-ray 8.3 7.9 6.6 6.2 8.1 7.8 6.6 6.2 1msy 27 X-ray 7.5 5.7 5.7 3.6 7.6 6.0 5.6 3.5 1nuj 24 X-ray 7.7 7.3 5.2 6.9 7.4 7.2 5.2 6.7 434d 14 X-ray 8.0 7.7 7.0 6.8 7.6 7.7 6.9 6.8 Normal modes (B) 1duq 26 X-ray 7.5 7.0 5.7 3.8 6.9 7.0 5.7 3.5 1esy 19 NMR 4.9 5.4 4.5 5.6 6.5 5.5 4.7 5.7 1f27 30 X-ray 5.9 5.8 3.7 2.6 6.7 5.8 3.7 2.5 1i9v 76 X-ray 6.1 2.6 5.3 3.0 5.5 2.7 5.1 3.0 1kka 17 NMR 5.7 4.6 4.1 4.6 6.9 4.3 4.1 4.8 1msy 27 X-ray 5.9 5.6 2.2 4.6 6.7 5.4 2.7 4.5 1nuj 24 X-ray 7.1 7.4 5.9 2.4 4.5 7.0 5.9 2.2 1qwa 21 NMR 3.5 3.2 2.0 3.8 3.7 3.3 2.2 3.9 1×9k 62 X-ray 6.7 1.6 5.2 3.0 3.1 1.9 5.2 2.8 1xjr 46 X-ray 7.7 5.4 7.9 2.2 6.2 5.0 7.9 2.5 1ykq 19 X-ray 4.6 3.4 3.5 2.8 5.0 3.3 3.8 2.5 1zih 12 NMR 7.7 5.4 5.7 6.6 6.9 5.3 5.7 6.5 28sp 28 NMR 5.7 4.0 6.5 1.8 5.7 4.5 6.7 2.9 2f88 34 NMR 6.8 5.4 4.9 4.4 4.1 5.4 4.7 4.2 434d 14 X-ray 7.7 7.4 7.4 5.2 6.9 7.4 7.6 5.2 FARNA (C) 1a4d 41 NMR 2.4 3.8 2.0 0.8 2.1 4.0 2.0 0.7 1csl 28 X-ray 2.0 1.5 1.6 1.3 2.4 1.4 1.6 1.4 1dqf 19 X-ray 4.2 1.8 2.8 1.0 3.6 2.0 3.2 1.0 1esy 19 NMR 3.2 3.7 4.8 1.2 3.8 3.5 4.2 1.1 1i9x 26 X-ray 3.4 1.3 2.2 1.5 4.0 1.5 3.6 1.6 1j6s 24 X-ray 0.2 1.4 0.2 0.6 1.6 1.7 0.8 0.5 1kd5 22 X-ray 3.2 0.3 0.8 0.2 2.4 0.5 1.6 0.3 1kka 17 NMR 1.4 1.2 0.6 0.6 2.0 0.8 0.8 0.6 1l2x 27 X-ray 0.6 3.2 1.0 1.8 1.5 3.2 1.2 1.8 1mhk 32 X-ray 1.6 1.2 1.6 1.0 1.4 1.2 1.4 1.2 1q9a 27 X-ray 2.6 0.5 0.8 0.8 3.2 0.5 1.2 0.8 1qwa 21 NMR 2.2 1.2 0.4 1.0 1.4 1.3 0.6 1.0 1xjr 46 X-ray 2.4 2.0 2.4 1.2 3.2 1.9 3.4 1.0 1zih 12 NMR 4.8 5.0 4.8 2 6.8 5.5 7.2 1.9 255d 24 X-ray 2.4 0.7 0.6 1.3 2.0 0.7 0.6 1.1 283d 24 X-ray 1.4 0.8 0.8 0.7 1.8 0.8 1.0 0.7 28sp 28 NMR 2.8 1.5 3.0 1.7 3.8 1.2 4.2 1.8 2a43 26 X-ray 2.2 2.0 1.4 0.6 3.2 1.8 2.0 0.6 2f88 34 NMR 3.2 1.3 2.2 1.3 3.6 1.3 1.6 1.2 Average values (A) 8.0 7.2 6.4 6.1 7.8 7.2 6.4 6.0 (B) 6.2 4.9 5.0 3.8 5.7 4.9 5.0 3.8 (C) 2.3 1.8 1.8 1.1 2.8 1.8 2.2 1.1 X-ray 4.8 3.8 3.7 2.8 4.7 3.8 3.9 2.7 NMR 4.2 3.5 3.5 2.7 4.4 3.5 3.7 2.8 All 4.5 3.7 3.6 2.7 4.6 3.7 3.8 2.7 Selecting correct structure containing non-canonical base pairs.

Publication Year: 2015