Pin Chen
Schrodinger (glide tools) software (2018-2 version) for docking,sitemap tools for binding sites predicting.
5YGX.pdb, 3 dimensions structure of ligand.
5YGX.pdb from PDB website.The ligand only gives the SMILES strings, ligprep tool in Schrodinger suites is used to obtain sd format file.
sitemap tools,docking twice,glide tools
It should be noted the docking box size, for one cocrytal ligand exited in 5YGX, but the size of this ligand is smaller than the docking ligands. Besides, the docking ligands are more complecated with many branched chains and aromatic rings. It will be better to use Sitemap tool to check the docking sites in the protein of 5YGX.
The docking site is not clearly in this case, firstly, using larger docking sites based on cocrytal ligand. After first docking, we found the docking site is clearly by viewing docking poses, and then we use more precisionly scoring to get dcking poses and poses ranking.
1).docking site with (18.94, 40.55, -6.39) extended by box with 30A, scoring function with low precision (SP-standard precision)
2).docking site with (25.86, 46.35, -10.64) extended by box with 20A, scoring function with high precision (XP-extra precison)
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Pin Chen
Schrodinger (2018-2)
docking, glide, XP-extra precison scoring function
Following the pose prediction process, structure-based method is used to obtain the final score. Here, we use the same grid file used in pose prediction step by docking site with (25.86, 46.35, -10.64) extended by box with 20A, scoring function with high precision (XP-extra precison)
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