Citations in PubMed

Primary Citation PubMed: 16288915 Citations in PubMed

PDB ID Mentions in PubMed Central Article count: 4

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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Biomolecular pleiomorphism probed by spatial interpolation of coarse models.

(2008) Bioinformatics 24

PubMed: 18757874 | PubMedCentral: PMC2732278 | DOI: 10.1093/bioinformatics/btn461

The rigid body docking of the complex identified the locations of the 14 monomers (PDB entry 1xck; Berman et al. , 2000 ) in the 3D map, and emphasized the conformational differences in the datasets (... Fig. 2 B).

Publication Year: 2008

Conformational sampling and nucleotide-dependent transitions of the GroEL subunit probed by unbiased molecular dynamics simulations.

(2011) PLoS Comput Biol 7

PubMed: 21423709 | PubMedCentral: PMC3053311 | DOI: 10.1371/journal.pcbi.1002004

A total of 21 crystal structures (287 GroEL subunits) were kept for further analysis (PDB-codes: 1PCQ, 1PF9, 1SVT, 3C9V, 1AON, 1GRU, 1MNF, 1XCK, 2C7D, 2NWC, 3E76, 2EU1, 1SS8, 1SX3, 1J4Z, 1KPO, 2C7E, 1... P8, 1OEL, 1WE3, 1WF4).

The atomic models were prepared from the high-resolution crystal structures with PDB codes 1XCK chain A [69] and 1SVT chain A [58] , for the closed and open forms, respectively.

Contact matrices were calculated for 28 closed (T) apo subunits (PDB code: 1XCK, 1SS8, 1OEL), 28 closed (T) ATP bound subunits (PDB code: 1KP8, 1SX3) and 28 open (R″) ADP bound subunits (PDB codes: 1AON, 1SVT, 1SX4, and 1PF9), and 6000 snapshots obtained from the last 50 ns of the 12 independent MD simulations on the closed GroEL subunit (6 apo and 6 holo).

The RMSd between the open and closed X-ray structure (PDB ids: 1SVT and 1XCK, respectively) is 12.30 Å.

Publication Year: 2011

A Bayesian view on cryo-EM structure determination.

(2012) J Mol Biol 415

PubMed: 22100448 | PubMedCentral: PMC3314964 | DOI: 10.1016/j.jmb.2011.11.010

The calculation of FSC curves between these maps and a fitted 2.9-Å GroEL crystal structure (Protein Data Bank ID: 1XCK , see Experimental Procedures ) confirmed that MAP refinement had reache... a higher resolution than the conventional approach ( Fig. 3 a, continuous lines).

The true resolution of the GroEL reconstructions was assessed by FSC with a published crystal structure (Protein Data Bank ID: 1XCK ).

Publication Year: 2012

RELION: implementation of a Bayesian approach to cryo-EM structure determination.

(2012) J Struct Biol 180

PubMed: 23000701 | PubMedCentral: PMC3690530 | DOI: 10.1016/j.jsb.2012.09.006

Reconstruction quality was assessed by FSC calculations between the reconstructed maps and a symmetrized GroEL crystal structure (PDB-ID 1XCK ) ( Bartolucci et al., 2005 ) that was also used to assess... GroEL reconstructions in a previous study ( Scheres, 2012 ).

Publication Year: 2012