Molecular docking is the most commonly used molecular simulation tool to explore the details of the interaction between any interacting biologically active molecules. However, which of the multiple possible conformations produced by the docking is the naturally occurring conformation? Determine the conformation, what force and the site of action play a key role?
There are two basis for determining the best conformation, one is the most binding pose, and the other is the best evaluation by the scoring function. However, if these two are a type of binding conformation (such as RMSD<2.0A), then it can be determined that this binding conformation is the best by more than 50% (according to experience). If you are not sure, you can determine it based on the existing pdb database data or references.
(1) First filter/ranking is usually the score of the pose. As the scoring function is a problem by itself for docking protocol.
(2) RMSD and the number of interacting residues and different type of interactions (hydrogen bonding, hydrophobic, lonic, Aromatic, Cation-π).
(3) Third is visual or empirical analysis analyzing: if you have a structure of your protein with a ligand, try to check if it is consistent. If not, check that the interactions you see are good.
Three 2D tools are recommended. Take protein ligand as an example. The 2D diagram shows that the ligand and the protein's amino acids have a clear interaction, mode of action and other information.
Poseview: In the PDB database, poseview is used to analyze the interaction of proteins and co-crystal ligands. The 2D map mapping effect is very good, but it is not free. There is a website here, htp://poseview.zbh.uni-hamburg. de/
Limitations: You can make a poseview diagram, but you can only analyze the hydrogen bonding between the ligand proteins.
Chimera and pymol:
The better thing about Chimera is that you can display the interacting amino acid residues by dragging the results in, which is very convenient.
Pymol can display the hydrogen bonding effect of the ligand protein, find --- polar contacts.
These softwares are installed and used on linux or windows 7/8/10.