Citations in PubMed

Primary Citation PubMed: 10986465 Citations in PubMed

PDB ID Mentions in PubMed Central Article count: 8

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

transFold: a web server for predicting the structure and residue contacts of transmembrane beta-barrels.

(2006) Nucleic Acids Res 34

PubMed: 16844989 | PubMedCentral: PMC1538872 | DOI: 10.1093/nar/gkl205

Formally, NWF consists of (PDB id) 1QJP, 1QJ8, 1THQ, 1P4T, 1I78, 1K24 and 1QD6, and WF of 1A0S, 1AF6, 1PRN, 2OMF, 1E54, 1TLY and 2POR.

Publication Year: 2006


Transmembrane protein alignment and fold recognition based on predicted topology.

(2013) PLoS One 8

PubMed: 23894534 | PubMedCentral: PMC3716705 | DOI: 10.1371/journal.pone.0069744

Figure 3(a) presents an example of αTMP Succinate Dehydrogenase (PDB_ID: 1NEK:D) [81] , and Fig. 3(b ) shows βTMP Omp32 (PDB_ID: 1E54:A) [82] .

Publication Year: 2013


A 3-dimensional trimeric ?-barrel model for Chlamydia MOMP contains conserved and novel elements of Gram-negative bacterial porins.

(2013) PLoS One 8

PubMed: 23935908 | PubMedCentral: PMC3723809 | DOI: 10.1371/journal.pone.0068934

Template Porin pdb code TMBPro Model Score 1 E. coli OmpF 2OMF 25,743 C. acidovarans Omp32 1E54 26,845 R. capsulatus Porin POR 30,812 R. pseudomonas Porin 1PRN 33,558 OmpF-Omp32 Hybrid 2OMF & ... E54 15,129 1 TMBpro search scores calculated as described in Randall et al.

Additional 16-stranded β-barrel crystal structure coordinates were added to the TMBpro template database manually for comparison of automated 3D MOMP output by the server; pdb codes 1OSM [35] , 1PHO [69] and 2J1N [64] and a composite template based on E. coli OmpF and C. acidovorans Omp32; residues A1 – R100 and F267 – F340 from 2OMF [69] and residues L94 – G250 from 1E54 [38] .

Publication Year: 2013


A Hidden Markov Model method, capable of predicting and discriminating beta-barrel outer membrane proteins.

(2004) BMC Bioinformatics 5

PubMed: 15070403 | PubMedCentral: PMC385222 | DOI: 10.1186/1471-2105-5-29

Protein name Number of β-strands PDB code [ 29 ] Organism OmpA 8 1QJP Escherichia coli OmpX 8 1QJ8 Escherichia coli OmpT 10 1I78 Escherichia coli OpcA 10 1K24 Neisseria Meningitidis OmpLA 12 1... D5 Escherichia coli Omp32 16 1E54 Comamonas Acidovorans OmpF 16 2OMF Escherichia coli Porin 16 2POR Rhodobacter capsulatus Porin 16 1PRN Rhodobacter blasticus Sucrose porin 18 1A0S Salmonella typhimurium Maltoporin 18 2MPR Salmonella typhimurium FepA 22 1FEP Escherichia coli FhuA 22 2FCP Escherichia coli FecA 22 1KMO Escherichia coli Table 2 Overall measures of accuracy, obtained in the Self-consistency and in the Jacknife testing.

Publication Year: 2004


A novel O-linked glycan modulates Campylobacter jejuni major outer membrane protein-mediated adhesion to human histo-blood group antigens and chicken colonization.

(2014) Open Biol 4

PubMed: 24451549 | PubMedCentral: PMC3909276 | DOI: 10.1098/rsob.130202

Here, we utilized the beta-barrel structure of the anion-selective porins of Comamonas acidovorans (1E54.

Publication Year: 2014


A real-time all-atom structural search engine for proteins.

(2014) PLoS Comput Biol 10

PubMed: 25079944 | PubMedCentral: PMC4117414 | DOI: 10.1371/journal.pcbi.1003750

One such scaffold (PDB ID = 1E54, colored light grey) possesses many exact residue/rotamer matches to the assembled fragment (blue highlights) and many close matches (yellow highlights... that differ by a related residue (threonine to serine or valine to isoleucine) or by varying the rotamer.

Publication Year: 2014


Differential contribution of tryptophans to the folding and stability of the attachment invasion locus transmembrane ?-barrel from Yersinia pestis.

(2014) Sci Rep 4

PubMed: 25266561 | PubMedCentral: PMC4179465 | DOI: 10.1038/srep06508

a,b PDB ID c Protein a,b # of β-strands d,e # of Trp residues Membrane interface Transmembrane Extra-membrane 1 1P4T NspA 10 (8) 0 - - - 2 2POR Porin 22 (16) 1 1 - - 3 3QRA Ail 9 (8) 2 1 1 - 4... 1QJ8 OmpX 8 (8) 2 1 1 - 5 2LHF OprH 10 (8) 2 2 - - 6 3HW9 OmpF 25 (16) 2 1 1 - 7 1E54 Omp32 24 (16) 2 - 1 1 8 3DZM TtoA 14 (8) 3 1 - 2 9 3FID LpxR 17 (12) 3 - 1 2 10 2X27 OprG 17 (8) 4 4 - - 11 3BRY TbuX 27 (14) 4 2 2 - 12 1K24 OpcA 15 (10) 4 3 1 - 13 1UYN NalP 14 (12) 4 3 - 1 14 1H6S Porin 19 (16) 4 3 1 - 15 3EMO Hia [6 (4)]x3 f 1 1 - - 16 4FQE KdgM 14 (12) 3 2 - 1 17 1UUN MspA [14 (2)]x8 f 4 3 1 - 18 3WI4 PorB [22 (16)]x3 f 4 3 - 1 19 1WP1 OprM [13 (4)]x3 f 4 2 - 2 20 2LME YadA [5 (4)]x3 f 2 1 - 1 a Non-redundant structures were retrieved from PDBTM: Protein Data Bank of Transmembrane Proteins; http://pdbtm.enzim.hu/ .

Publication Year: 2014


Evaluation of methods for predicting the topology of beta-barrel outer membrane proteins and a consensus prediction method.

(2005) BMC Bioinformatics 6

PubMed: 15647112 | PubMedCentral: PMC545999 | DOI: 10.1186/1471-2105-6-7

Protein name Number of β-strands PDB ID Reference Organism NspA 8 1P4T [67] Neisseria Meningitidis OmpX 8 1QJ8 [68] Escherichia coli Pagp 8 1MM4 [69] Escherichia coli OmpA 8 1QJP [50] Escheric... ia coli OmpT 10 1I78 [70] Escherichia coli OpcA 10 1K24 [71] Neisseria Meningitidis Nalp 12 1UYN [41] Neisseria Meningitidis OmpLA 12 1QD5 [72] Escherichia coli Porin 16 2POR [73] Rhodobacter capsulatus Porin 16 1PRN [74] Rhodopseudomonas blastica OmpF 16 2OMF [75] Escherichia coli Osmoporin 16 1OSM [76] Klebsiella pneumoniae Omp32 16 1E54 [77] Comamonas Acidovorans Phosphoporin 16 1PHO [78] Escherichia coli Sucrose porin 18 1A0S [79] Salmonella typhimurium Maltoporin 18 2MPR [80] Salmonella typhimurium FhuA 22 2FCP [46] Escherichia coli FepA 22 1FEP [47] Escherichia coli FecA 22 1KMO [48] Escherichia coli BtuB 22 1NQE [49] Escherichia coli Table 6 The available predictors, used for predicting the transmembrane strands of β-barrel outer membrane proteins.

Publication Year: 2005