Fig 1.
Description of hydrophobic interactions on the contact surface.
Hydrophobic and hydrophilic grid points are represented by blue and red circles, respectively, on the SAS of the ligand. Hydrophobic grid points within the van der Waals surface of hydrophobic residues are marked by filled blue circles.
Fig 2.
Scatter plots of log RBA calculated for 31 training ligands (A, B, and C) and 111 external test ligands (D). Protein-ligand complex structures were obtained from crystal structures (A), self-docking (B), cross-docking (C), and single or three receptor structures-based docking (D).
Table 1.
Summary of pharmacophore, fingerprint, and QSAR model parameters.
Table 2.
Accuracy as rank of binding mode prediction based on the 3D-QSAR combined with self-docking or cross-docking.
Fig 3.
Classification of His524 conformations (PDB IDs: 2YJA, 4IVY, and 4IWC).
Closed (A) and moved back (B) conformations which stabilize protein-ligand complex through hydrogen bond and hydrophobic interaction, respectively. Open conformation (C) that provides an expanded binding pocket for ligands longer than 13 Å. Ligands are colored in orange with hydrogen, oxygen, nitrogen, sulfur, and fluorine atoms in white, red, blue, yellow, and green, respectively.
Fig 4.
Hydrophobic contacts (log PC) of n-alkyl group vs log RBA residual of n-alkyl 4-phenol (gray circles) and n-alkyl paraben (black filled circles).
Fig 5.
Prediction of RBA of 17β-estradiol derivatives based on protein-ligand complex structures from crystal structure modification (blue bars) or molecular docking (red bars).
RBA is described by contributions from hydrophobic contacts (rectangle bars) and hydrogen bonds (hexagon bars). Black dots represent the experimental log RBA.