Citations in PubMed

Primary Citation PubMed: 10742169 Citations in PubMed

PDB ID Mentions in PubMed Central Article count: 2

Citations in PubMed

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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.

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Automated 3D structure composition for large RNAs.

(2012) Nucleic Acids Res 40

PubMed: 22539264 | PubMedCentral: PMC3413140 | DOI: 10.1093/nar/gks339

Quality of predicted RNA 3D models a RNA PDB code and chain Strand length (nt) Accuracy b Precision c r.m.s.d. (Å) INF a ll INF c b p r.m.s.d. (Å) Hairpin    &#... 02003;2DR8 B 33 1.7 0.88 1.00 1.4     3OVA C 34 3.2 0.79 1.00 2.0 Hairpin, internal loop     1JBR D 31 4.4 0.74 0.98 2.7     2HW8 B 36 2.8 0.86 1.00 1.4     1ZHO B 38 2.0 0.83 0.99 1.1     3IAB R 46 11.0 0.72 0.88 1.2 Hairpin, internal loops     1I6U C 37 2.7 0.79 0.99 2.0     2PXL B 47 2.3 0.84 1.00 2.1     2VPL B 48 4.7 0.81 0.97 1.7     2PXB B 49 3.7 0.84 1.00 2.1     1MZP B 55 2.5 0.78 0.99 1.7     1KXK A 70 9.7 0.75 0.97 5.0 Three-way junction     1DK1 B 57 4.1 0.82 0.98 2.4     1MMS C 58 3.1 0.73 0.97 2.3     1UN6 E 61 4.0 0.80 0.88 2.2 Three-way junction (hammerhead)     2QUS A 69 3.8 0.81 0.96 1.6 Three-way junction (riboswitch)     3LA5 A 71 1.9 0.87 1.00 1.0     3D2V A 77 3.3 0.82 0.99 2.0 Three-way junction (GMP riboswitch)     3IWN A 93 3.9 0.75 0.97 2.3 Three-way junction (SRP)     2V3C M 96 10.0 0.76 0.94 3.0     1LNG B 97 6.6 0.77 0.99 2.6     1Z43 A 101 4.8 0.76 0.98 2.7     3NDB M 136 7.2 0.80 0.96 4.2 Three-way junction (5S rRNA)     3OFQ B 117 4.0 0.75 0.90 2.3     3OFR B 118 4.1 0.83 1.00 3.2     3KIR B 119 5.1 0.77 0.94 4.4     3I9E B 120 5.0 0.81 0.96 3.3     1VQO 9 122 3.3 0.84 1.00 2.6 Four-way junction (tRNA)     1EXD B 73 2.9 0.77 1.00 2.3     1U0B A 74 7.1 0.69 0.99 2.5     1FFY T 75 2.1 0.82 0.96 1.4     2J00 W 76 3.2 0.73 0.95 2.2 Four-way junction (riboswitch)     3IQP A 94 3.1 0.81 0.99 2.2 Five-way junction (tRNA)     3AM1 B 81 5.4 0.78 0.99 3.9     1WZ2 C 88 20.5 0.66 1.00 5.1     3ADB C 92 4.7 0.67 1.00 2.8 Pseudoknot     2QWY A 52 11.2 0.54 0.98 2.2 Pseudoknot (HDV ribozyme)     1CX0 B 72 2.7 0.83 0.97 1.6 P4–P6 ribozyme domain     2R8S R 159 15.2 0.76 0.99 7.9 M-box riboswitch     3PDR A 161 3.2 0.81 1.00 1.3 a Upon validation, all the 3D structure elements comprised by the respective crystal PDB structure were excluded from the dictionary.

Publication Year: 2012


Predicting helical topologies in RNA junctions as tree graphs.

(2013) PLoS One 8

PubMed: 23991010 | PubMedCentral: PMC3753280 | DOI: 10.1371/journal.pone.0071947

PDB Degree Native Structure RNAJAG Nts RNA Type Coaxial Stacks Family Type Coaxial Stacks Family Type RMSD (Å) Max Angle (°) 2FK6 52 tRNA 3WJ H 1 H 3 C H 1 H 3 A 4.01 166.43 1DK1 57 rR... A 3WJ H 2 H 3 A H 2 H 3 A 6.16 65.70 1MMS 58 rRNA 3WJ H 1 H 3 C H 1 H 3 C 4.13 16.36 3EGZ 65 Riboswitch 3WJ H 2 H 3 C H 2 H 3 C 6.59 46.63 2QUS 64 Ribozyme 3WJ H 1 H 3 C H 1 H 2 C 10.40 159.06 2OIU 51 Ribozyme 3WJ H 1 H 2 A H 1 H 2 A 2.12 28.98 3D2G 77 Riboswitch 3WJ H 1 H 2 A H 1 H 2 A 2.07 45.90 2HOJ 78 Riboswitch 3WJ H 1 H 2 A H 1 H 2 A 2.18 52.36 2GDI 80 Riboswitch 3WJ H 1 H 2 A H 1 H 2 A 1.98 58.95 1LNG 97 7S.

Publication Year: 2013