Primary Citation PubMed: 9813012
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A restraint molecular dynamics and simulated annealing approach for protein homology modeling utilizing mean angles.
(2005) BMC Bioinformatics 6
PubMed: 15819976 | PubMedCentral: PMC1127110 | DOI: 10.1186/1471-2105-6-91
Table 2 Statistics of PDB structure files used for Ppar γ PDB code Organism Method Resolution [nm] Reference 3PRG human X-ray 0.29  1K7L human X-ray 0.25  1KKQ human X-ray 0.30  1I... G human X-ray 0.22  1GWX human X-ray 0.25  3GWX human X-ray 0.24  Table 3 Restraints for molecular dynamics calculation for HPr Type of restraint Number inter-atomic distances 186 hydrogen bonds 50 backbone dihedral angles 164 Table 4 Restraints for molecular dynamics calculation for Ppar γ Type of restraint Number inter-atomic distances 1391 hydrogen bonds 153 backbone dihedral angles 528 Table 5 Structural statistics for HPr RMSD values for the ten lowest-energy structures RMSD [nm] backbone atoms C α , C', N 0.041 heavy atoms 0.111 Residues in the Ramachandran plot Incidence a most favored regions 87.2 % additional allowed regions 12.8 % generously allowed regions 0.0 % disallowed regions 0.0 % a The dihedral angles have been analyzed using the program PROCHECK-NMR.
For Ppar γ the best model structure in terms of pseudo-energy was compared to the target X-ray structure (3PRG).
Publication Year: 2005
PubMed ID is not available.
Published in 2015
As there are missing residues in 1GWR and 3PRG, Discovery Studio 2.5.5 (DS 2.5.5, Accelrys Inc., San Diego, CA) was used to add these missing residues in the loop regions.
Materials and Methods Preparation of the initial structures for molecular dynamics simulations The atom coordinates of the complexes of hERα-BPA (PDB code: 3UU7 [ 11 ], 2.2 Å), hERα-estradiol (PDB code: 1GWR [ 35 ], 2.4 Å), hERRγ-BPA (PDB code: 2E2R [ 19 ], 1.6 Å) and hPPARγ (PDB code: 3PRG [ 36 ], 2.9 Å) were obtained from the RCSB Protein Data Bank.
Publication Year: 2015
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