Primary Citation PubMed: 7781068
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Protein structure prediction by all-atom free-energy refinement.
(2007) BMC Struct Biol 7
PubMed: 17371594 | PubMedCentral: PMC1832197 | DOI: 10.1186/1472-6807-7-12
Decoy sets and relaxation The decoy sets were provided electronically by J. Tsai [ 6 ], we have excluded decoy sets that contained only fragments of the experimental structure (2ptl,1tuc,1vcc), that c... ntain iron clusters, stabilizing ions or heavy metals not parametrized in our forcefield (1bq9, 1cc5, 1ptq, 1tif, 5icb).
Publication Year: 2007
Atomic hydration potentials using a Monte Carlo Reference State (MCRS) for protein solvation modeling.
PubMed: 17397537 | PubMedCentral: PMC1852318 | DOI: 10.1186/1472-6807-7-19
Among unrecognized structures, e.g. 1ptq has a large hydrophobic patch at its surface and lacks a clearly defined hydrophobic core, whereas 1a32 has a loose packing with a number of hydrophobic groups... accessible to the solvent.
Intrinsically disordered regions may lower the hydration free energy in proteins: a case study of nudix hydrolase in the bacterium Deinococcus radiodurans.
(2010) PLoS Comput Biol 6
PubMed: 20657662 | PubMedCentral: PMC2904767 | DOI: 10.1371/journal.pcbi.1000854
The PDB codes of the proteins from the representative data set and their PMVs are: 1PTQ (4151.81 cm3/mol), 1UB9 (8458.46 cm3/mol), 1I39 (16735.06 cm3/mol), 1HCZ (20052.73 cm3/mol), 1RU4 (30743.60 cm3/... ol), 1A8H (42650.21 cm3/mol), and 1EX1 (48276.45 cm3/mol).
Publication Year: 2010
Solving the molecular distance geometry problem with inaccurate distance data.
(2013) BMC Bioinformatics 14 Suppl 9
PubMed: 23901894 | PubMedCentral: PMC3698034 | DOI: 10.1186/1471-2105-14-S9-S7
〈 TIME 〉 PDB lsbuild buildup dgsol 1PTQ 9.99E-01 5.34E-01 1.03E+01 1LFB 1.86E+00 1.01E+00 2.55E+01 1AX8 2.98E+00 1.70E+00 4.36E+01 1F39 7.21E+00 3.57E+00 8.59E+01 1RGS 1.43E+01 4.70E+0... 1.33E+02 1KDH 2.12E+01 7.28E+00 2.09E+02 1BPM 2.47E+01 8.04E+00 2.99E+02 1TOA 3.93E+01 1.14E+01 7.03E+02 1MQQ 3.93E+01 1.82E+01 7.63E+02 The mean CPU time in seconds with the instances considering just 70% of the distances below 6Å.
〈 LDME 〉 〈 RMSD 〉 PDB | V | lsbuild buildup dgsol lsbuild buildup dgsol 1PTQ 402 2.61E-03 1.80E+00 5.41E-01 1.31E-02 9.49E+00 6.89E+00 1LFB 641 2.03E-04 1.84E+00 3.91E-01 4.19E-03 1.23E+01 5.48E+00 1AX8 1003 2.00E-04 1.83E+00 4.33E-01 1.62E-02 1.35E+01 7.95E+00 1F39 1534 3.03E-02 1.89E+00 4.74E-01 4.22E-01 1.79E+01 1.28E+01 1RGS 2015 1.08E-01 1.87E+00 4.73E-01 1.74E+00 1.92E+01 1.35E+01 1KDH 2846 1.39E-02 1.86E+00 5.19E-01 9.43E-02 2.11E+01 1.61E+01 1BPM 3671 2.20E-02 1.90E+00 5.14E-01 7.86E-02 2.29E+01 1.55E+01 1TOA 4292 6.90E-03 1.89E+00 6.75E-01 2.56E-01 2.52E+01 2.39E+01 1MQQ 5681 1.93E-02 1.91E+00 8.86E-01 1.89E-01 2.50E+01 2.50E+01 Results with instances considering just 70% of the distances below 6Å.
Publication Year: 2013
Single-molecule studies reveal a hidden key step in the activation mechanism of membrane-bound protein kinase C-?.
(2014) Biochemistry 53
PubMed: 24559055 | PubMedCentral: PMC3971957 | DOI: 10.1021/bi4016082
The indicated protein structures are based on crystal structures of PDB entries 3PFQ( 28 ) and 1PTQ.
Publication Year: 2014
PubMed ID is not available.
Published in 2015
This figure was generated from pdb entry 1PTQ [ 95 ] using the UCSF Chimera package [ 136 ].
Publication Year: 2015
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