A rigid body refinement was used with the structure of the hVDR LBD complexed to 1α,25(OH)2D3 as a starting model.
Occipital also bundles a few other in-house apps for gaming and other applications to use with the Structure Sensor.
In [16], the authors suggest an alternative proposal construction considering pieces of second order polynomial, in order to be used with the ARMS structure [12].
The peptide termini were unprotected in agreement with the experimental conditions used with the 2DX2 structure.
To generate a total of 100 decoy sets, MODELLER was used with the selected template structure.
Default settings were used with the admixture model of STRUCTURE, run for 300,000 steps (the first 100,000 discarded as burn-in).
PSIPred 2.5 was used with the uniref90 database for secondary structure prediction.
Phases were obtained by molecular replacement using PHASER with the structure of the Fab KcsA complex [Protein Data Bank (PDB) entry 1K4C] as the search model.
First, a homology model of the complex was directly generated using Modeler with the structure of the RPA32C UNG2 peptide complex as a template.
Structures were determined by molecular replacement using PHASER with the structure of the p300/Lys-CoA complex (Protein Data Bank entry 3BIY) with the Lys-CoA inhibitor removed as a search model.
