Citations in PubMed

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PDB ID Mentions in PubMed Central Article count: 6

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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Stereophysicochemical variability plots highlight conserved antigenic areas in Flaviviruses.

(2005) Virol J 2

PubMed: 15845145 | PubMedCentral: PMC1112618 | DOI: 10.1186/1743-422X-2-40

b) Stereochemical variability plot (SVP) of the DV2-Env (PDB file 1OKE), showing the per residue variation across the Flaviriridiae.

Publication Year: 2005


Combinatorial computational approaches to identify tetracycline derivatives as flavivirus inhibitors.

(2007) PLoS One 2

PubMed: 17502914 | PubMedCentral: PMC1855430 | DOI: 10.1371/journal.pone.0000428

g001 Figure 1 Pre-fusion (PDB code 1oke) and post-fusion (PDB code 1ok8) conformations of Dengue virus E protein and the ligand-binding pocket for virtual screening.

The crystal structures of the E protein of DV type 2 in both the presence (pre-fusion) and absence (post-fusion) of a bound ligand were deposited in the Protein Data Bank {PDB codes 1oke [5] and 1ok8 [11] , respectively; Figure 1 ).

To reduce the complexity and running time of the computational program, we isolated the structure of the BOG binding pocket of the DV E protein ( Figure 1B ) in the BOG-bound conformation {PDB code 1oke [5] } and prepared it for the docking tools.

(A) TetR protein (PDB code 2TRT); (B) DV E protein (PDB code 1OKE).

Publication Year: 2007


Extensive structural change of the envelope protein of dengue virus induced by a tuned ionic strength: conformational and energetic analyses.

(2012) J Comput Aided Mol Des 26

PubMed: 23160852 | PubMedCentral: PMC3532723 | DOI: 10.1007/s10822-012-9616-4

Two experimental structures of the E protein, namely pdb id 1oke and 1oan, are shown in Fig.

Methods The systems were settled by inserting the E protein monomer of the DENV2 (pdb id 1oke) in the center of a parallelepiped box of sides 8.0, 9.0 and 16.0 nm.

The E protein structure was determined by X-ray diffraction of crystals produced at basic pH in a medium of ionic strength greater than 1 M (one molar); pdb id: 1oke and 1oan [ 25 , 26 ].

b Superposition of the experimental structures 1oan ( cyan ) and 1oke shows that the binding of β-OG molecule ( red spheres )—at the boundary of DI and DII—causes a minor locally rearrangement of the β-hairpin (residues 268–280) Images were created using the Pymol free version (available at: http://www.pymolwiki.org/index.php/Main_Page ), Swiss-PdbViewer (available at http://spdbv.vital-it.ch/ ) and VMD (available at: http://www.ks.uiuc.edu/Research/vmd/ ).

Publication Year: 2012


New pockets in dengue virus 2 surface identified by molecular dynamics simulation.

(2013) J Mol Model 19

PubMed: 23197323 | PubMedCentral: PMC3578724 | DOI: 10.1007/s00894-012-1687-6

However, the monomers of the dimer DENV-2 E protein structure, under the PDB code 1OKE [ 18 ], present smaller RMSDs, 0.25 nm and 0.26 nm for the A and B chains of 1THD.

The smaller RMSD and the advantage of the good intermonomer contacts in 1OKE are advantages taken into account in the T structure construction, by means of the better C α superposition of 1OKE on the dimer formed by the B and C chains of 1THD and by the best superposition of the A chain of 1OKE on the A chain of 1THD, as shown in Fig.

These pockets, which are also found in the crystallographic 1OKE structure, are located along the interface between DI and DIII within the same chain.

The values are depicted in the average structure in which the size of the radius of the chain corresponds to RMSD res The presence of pockets was first tested on the experimental structure of the DENV-2 E protein (1OKE) dimer, with the objective of verifying whether the methodology was able to find the binding site where the β -OG detergent is located, at the junction of the DI and DII domains of both monomers [ 18 ].

The sugar molecules, the β -OG detergent, and the water molecules were removed from the 1OKE structure, allowing an investigation of the protein pockets without interferences.

Publication Year: 2013


Sulfated polysaccharide, curdlan sulfate, efficiently prevents entry/fusion and restricts antibody-dependent enhancement of dengue virus infection in vitro: a possible candidate for clinical application.

(2013) PLoS Negl Trop Dis 7

PubMed: 23658845 | PubMedCentral: PMC3636050 | DOI: 10.1371/journal.pntd.0002188

The coordinates of the DENV E protein were obtained from PDB from the crystal structure 1OKE [13] .

Materials and Methods Blind docking study of CRDS with DENV E protein The coordinates of the DENV E protein were obtained from PDB from the crystal structure 1OKE [13] .

Accession numbers The Protein Data Bank (PDB) accession code for the DENV-2 Envelope protein used for the computational modeling in this paper is 1OKE [13] .

Publication Year: 2013


Carbohydrate-related inhibitors of dengue virus entry.

(2013) Viruses 5

PubMed: 23389466 | PubMedCentral: PMC3640517 | DOI: 10.3390/v5020605

The structure of EGP based on the three-dimensional structure of PDB accession number 1OKE.

Publication Year: 2013