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. 2015 Apr 14;43(Web Server issue):W443–W447. doi: 10.1093/nar/gkv315

Figure 3.

Figure 3.

Example illustrating the four steps of PLIP in interaction detection for palmitic acid in Bacillus subtilis DegV protein (PDB ID 3FYS). (A) Structure preparation and detection of relevant ligands. (B) Functional characterization of molecules, here shown for the assignment of charges to amino acid side chains and the ligand carboxyl group. (C) Matching of interacting atoms using a rule-based system of geometric constraints. In the case of salt bridges, the distance between attracting charges is measured. (D) Filtering steps to minimize the number of depicted interactions, particularly important in the case of hydrophobic contacts (shown as solid gray lines).