标题: Compatibility between 3D & 2D visualisation of interactions protein-ligand [打印本页] 作者Author: zako 时间: 2020-11-6 19:07 标题: Compatibility between 3D & 2D visualisation of interactions protein-ligand Hello Dears,
I performed a docking analysis, and i used the Protein-Ligand Interaction Profiler (PLIP) web server for the visualisation of the 3D interactions, and i also need the the 2D interaction diagram, for that i used the discovery studio, the problem that i faced is that i didn't found any compatibility between the 3D and 2D visualisation, i must find the same interactions in 3D and 2D for publication purpose.
I need your helps in this matter.
Sincerely,
作者Author: sobereva 时间: 2020-11-7 17:48
I suggest using ligplot or https://proteins.plus to generate 2D interaction map, they are freely available. Then, using VMD to plot a proper 3D structure map, and then manually label interactions between residues and ligand (using e.g. photoshop, powerpoint) according to the 2D map. However, note that 2D map is sometimes misleading or too idealized, and it is not always compatible with the more realistic 3D map.