Citations in PubMed

Primary Citation PubMed: 18456657 Citations in PubMed

PDB ID Mentions in PubMed Central Article count: 5

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.

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RNAMotifScan: automatic identification of RNA structural motifs using secondary structural alignment.

(2010) Nucleic Acids Res 38

PubMed: 20696653 | PubMedCentral: PMC2952876 | DOI: 10.1093/nar/gkq672

To demonstrate this, we selected three PDB entries with different resolutions for the same 16S rRNA structure from Thermus thermophilus (PDBid: 2VQE, 1J5E and 1I95), and used RNAMotifScan to identify ... he five motifs in them.

bp #KT #CL #SR #RK #EL 2VQE 2.50 Å 1522 766 433 333 3 0 2 0 6 1J5E 3.05 Å 1522 761 434 327 2 0 2 0 6 1I95 4.50 Å 1514 699 422 277 1 0 0 0 3 The columns in the tables represent PDB codes of the RNA structures, the resolution, the length, the number of base pairs (bp) annotated by MC-Annotate, the number of annotated canonical base pairs (Can.

Since the RNA structure from 2VQE contains three RNA chains, while the other two structures contain only one RNA chain, we only consider their common RNA chain (chain A in the comparison).

Publication Year: 2010


Toward the estimation of the absolute quality of individual protein structure models.

(2011) Bioinformatics 27

PubMed: 21134891 | PubMedCentral: PMC3031035 | DOI: 10.1093/bioinformatics/btq662

Indeed, the peptides with the highest, i.e. most unfavourable, energies in the dataset are the ribosomal protein THX [PDB:2vqe, ( Kurata et al. , 2008 )] and the disordered protein hypocretin presente... on a MHC class II protein [PDB:1uvq ( Siebold et al. , 2004 )].

Publication Year: 2011


HD-RNAS: An Automated Hierarchical Database of RNA Structures.

(2012) Front Genet 3

PubMed: 22529851 | PubMedCentral: PMC3329738 | DOI: 10.3389/fgene.2012.00059

Query Length Original function Best match Predicted function Best score Average SD Prediction score 1FIR-A 76 tRNA Lys 1EVV-A tRNA Phe 362.00 131.60 13.62 16.92 2B57-A 65 Riboswitch 2XNZ-A Riboswitch ... 07.00 99.34 11.35 18.29 2ZZM-B 88 tRNA Leu 1WZ2-D tRNA Leu 326.50 118.16 14.40 14.46 2ZZN-C 75 tRNA Cys 3KFU-L tRNA Asn 304.00 128.54 12.98 13.52 2ZZN-D 75 tRNA Cys 1F7U-B tRNA Arg 309.00 135.00 13.32 13.06 3KIQ-a 1504 rRNA 2VQE-A 16S rRNA 5904.50 2062.09 46.95 81.85 3KIQ-v 77 tRNA 2FMT-D tRNA Fmet 349.00 150.39 15.36 12.93 3KIR-A 2848 rRNA 2XG0-A rRNA fragment 12839.00 3764.09 55.97 162.13 3KIR-B 119 rRNA 2J01-B 5S rRNA 505.00 156.37 13.11 26.60 3KIS-a 1504 rRNA 2VQE-A 16S rRNA 5904.50 2068.17 46.28 82.89 3KIS-v 77 tRNA 2ZUE-B tRNA Arg 342.00 146.26 11.99 16.32 3KIT-A 2848 rRNA 2XG0-A rRNA fragment 12821.00 3779.68 61.28 147.53 3KIT-B 119 rRNA 2J01-B 5S rRNA 523.00 148.25 13.61 27.54 3KNN-W 75 tRNA 1F7U-B tRNA Arg 279.00 129.06 12.13 12.36 3KNN-X 77 tRNA Fmet 2FMT-D tRNA Fmet 331.00 147.96 14.51 12.62 1VFG-D 75 Primer tRNA 2V0G-F tRNA Leu 138.00 93.55 8.51 5.22 3KNN-Y 75 tRNA 2XQD-W tRNA 208.00 146.06 11.57 5.35 3MOJ-A 74 23S rRNA 2XG0-A rRNA fragment 196.50 158.28 8.48 4.51 3NPB-A 119 Riboswitch 2A64-A Ribonuclease 318.00 255.50 15.32 4.08 3R9X-C 35 16S rRNA 1M5O-E Ribozyme 142.00 83.44 13.25 4.42 3KIS-w 77 tRNA 2XG0-A rRNA fragment 164.50 160.35 12.56 0.33 3KIQ-w 77 tRNA 2XG0-A rRNA fragment 211.00 203.98 10.29 0.68 1P6V-B 68 tmRNA 2XG0-A rRNA fragment 146.00 107.33 8.65 4.47 1P6V-D 68 tmRNA 3IAB-R Ribonuclease 102.00 65.03 10.56 3.50 1S03-A 47 mRNA 2ZNI-D tRNA Lys 178.50 127.49 9.00 5.67 1S03-B 47 mRNA 2ZNI-D tRNA Lys 178.50 127.83 9.54 5.31 1VFG-C 75 Primer tRNA 2XG0-A rRNA fragment 123.50 105.85 6.09 2.90 Table 5 Function annotation to unannotated RNAs .

Publication Year: 2012


A structural basis for streptomycin-induced misreading of the genetic code.

(2013) Nat Commun 4

PubMed: 23322043 | PubMedCentral: PMC3552334 | DOI: 10.1038/ncomms2346

Potential positions of magnesium or potassium ions were compared with those in a high-resolution (2.5 Å) 30S subunit structure (PDB accession code 2VQE 44 ) in Coot 45 , and positions with str... ng difference density were retained.

Coordinates of the 30S subunit structure (PDB accession code 1J5E 12 ) with additional RNA and protein modifications were used for initial rigid body refinement with Phenix 14 for the Apo, Strep, and Par data sets (PDB accession code 2VQE 44 ) was used for all other data sets).

Publication Year: 2013


PubMed ID is not available.

Published in 2015

PubMedCentral: PMC4529986

Table 4 Protein-RNA complexes in RB344 dataset RNA category PDB ID RNAse 2BX2 2IX1 2NUG 2QKB 2XDB 2Y8Y 3BSU 3IAB 3T3O 3ULD 4 AM3 4ATO SRP 1E8O 1HQ1 1JID 1LNG 1MFQ 2V3C 3KTW Aptamer 1OOA 3AGV 3... D2 3V7E dsRNA 1DI2 2YKG 3CIY 3EQT 3LRR 4IG8 Exosome 2JEA 2PO1 2VNU 4IFD mRNA 1FXL 1GTF 1MSW 1UVM 1WPU 1WSU 1ZH5 2A8V 2F8K 2IPY 2J0S 2O5I 2PJP 2Q66 2VPL 2XGJ 2XNR 2XS2 2XZO 3BX2 3D2S 3I5X 3ICE 3MDI 3NMR 3P6Y 3PEY 3PO3 3Q0Q 3QGC 3R2C 3RER 4 F02 4HXH 4J7L 4JVY Ribosomal 1DFU 1FEU 1FKA 1HR0 1I6U 1JBS 1MJI 1MMS 1MZP 1NKW 1SDS 1T0K 1UN6 1VQ8 1VQO 1Y69 2ASB 2BH2 2D3O 2 J01 2QA4 2VQE 2XFZ 2ZJQ 2ZJR 3AEV 3DH3 3F1E 3HUW 3I8I 3IEV 3KIS 3MOJ 3OIN 3R8S 3R8T 3R9X 3SFS 3SGF 3UMY 3 V24 3 V26 3V2C 3V2D 3V2F 3ZN9 4DH9 4GD1 4JUW 4JUX Small 1SI3 1YVP 2BGG 2F8S 3A6P 3ADI 3HO1 3HTX 3 MJ0 3NMU 3NVI 3O7V 3VYX 3VYY 3ZC0 4F1N 4KRE snRNP 1M8V 1URN 2OZB Splicing 1A9N 2G4B tRNA 1ASY 1B23 1C0A 1F7U 1FFY 1GAX 1H3E 1H4S 1J1U 1J2B 1K8W 1 N78 1Q2R 1QF6 1QTQ 1R3E 1SER 1U0B 1VFG 1WZ2 2AZX 2B3J 2CT8 2CZJ 2D6F 2DER 2DLC 2DU3 2FK6 2FMT 2GJW 2I82 2IY5 2ZNI 2ZUE 2ZZM 3AL0 3 AM1 3AMT 3BT7 3EPH 3FOZ 3HL2 3ICQ 3KFU 3OVB 3QSY 3TUP 3VJR 3W3S 3ZGZ 4ARC Viral 1A34 1AV6 1DDL 1F8V 1HYS 1KNZ 1 N35 1PGL 1R9F 2AZ2 2BU1 2GIC 2GTT 2JLV 2QUX 2R7W 2W2H 2WJ8 2Z2Q 2ZI0 2ZKO 3AVX 3BSO 3KMQ 3 L25 3O8C 3RW6 3T5N 4FY7 4GV9 4H5P 4HKQ 4J1G 4K4Z Other 1EC6 2ANR 2DB3 2GJE 2GXB 2PY9 2R8S 2XLK 3AF6 3HAX 3IEM 3PF4 3PKM 3QJL 3RC8 3S14 4B3G 4ERD 4FXD 4GG4 4ILL PDB ID of protein-RNA complexes in RB344 dataset Identification of protein surface residues To determine protein surface residues, accessible areas will be computed first.

Publication Year: 2015