Fig. 4.

Calculating LBias SIM score. A query protein Q is shown at Left with three atoms, q₁, q₂, and q₃, identified specifically. The second panel shows a ligand-containing protein NL, structurally similar to Q with the ligand shown as a gray line connecting two gray atoms. Ligand-binding residues, n₁ and n₂, are identified. The NL complex is superposed onto Q. Residues from Q that interact with the superposed ligand are identified (q₁ and q₂ in the above). A protein–ligand similarity score between QL and NL (S_QL:NL) is then calculated, where $S_{QL:NL}=m_{11}{e}^{-\gamma r_{11}^2}+m_{12}{e}^{-\gamma r_{12}^2}+m_{21}{e}^{-\gamma r_{21}^2}+m_{22}{e}^{-\gamma r_{22}^2}$. S_QL:NL is a function of all of the pairwise distances (e.g., r₁₁, r₁₂) between the atoms from Q interacting with the superposed ligand and the atoms from N interacting with the native ligand if the two atoms in question make chemically similar contacts with the ligands. For example, if n₁ makes a hydrogen bond with the ligand, but q₁ is hydrophobic, m₁₁ would be zero and there would be no contribution to S_QL:NL from this pair of atoms (Materials and Methods).