Difference FragMaps

The difference between SILCS FragMaps of structurally similar proteins can provide insights into differences in their activities. The SilcsBio software provides a utility in the command line interface (CLI) to calculate the difference between two SILCS FragMaps. The resulting difference FragMaps are a powerful tool to qualitatively analyze the difference between the functional group affinity pattern on two similar proteins including, but not limited to, kinases, BCL2 proteins, and mutants of the same protein.

A qualitiative analysis to investigate the differences in similar proteins may be accomplished by visualizing the difference FragMaps, which will offer insights into regions of the protein more favorable or less favorable for certain functional groups. Such information may be used to design molecules highly specific for only one protein (or dual specific for both proteins) or facilitate the identification and design of agonists versus antagonists, such as for GPCRs. See references [12] or [25] for example applications of difference FragMaps. The two-step procedure for calculating difference FragMaps is described below.

1. Copy the two silcs_fragmaps_<protein PDB> directories you wish to use to a new directory in which the difference calculations will be performed.

   Please make sure that the FragMaps meet one of the following criteria:

   • Both sets of FragMaps have the same grid setup, which means the header of the silcs_fragmaps_<protein PDB>/maps/*.map files are the same.

   • Both sets of FragMaps have were created relative to proteins having the same rotational and translational alignments. If the input proteins were not aligned to each other prior to running SILCS, you must use the “ref=” option with the 2b_gen_maps command to ensure alignment. A map cutting algorithm will be used to make the FragMaps compatible, with the smaller dimensions of the two grids used to calculate the difference FragMaps.

   Warning

   It is imperative that the two SILCS FragMaps used to calculate difference FragMaps are oriented to structurally aligned proteins. Difference FragMaps that result from incompatible FragMaps will not provide any useful insights.

2. Generate the difference FragMaps using the following command:

   $SILCSBIODIR/utils/calc_difference_maps.sh <silcs_fragmaps_#1> <silcs_fragmaps_#2>
   

   The difference FragMaps will be saved in a directory DIFF_MAPS_<fragmap#1>_VS_<fragmap#2> and can be visualized in the same way as standard FragMaps (Visualizing SILCS FragMaps).

Tip

The difference in GFE values are calculated as <silcs_fragmap_#1> - <silcs_fragmap_#2>. In the difference FragMaps, if the value at a grid point is negative, the grid free energy (GFE) of the grid point in <silcs_fragmap_#1> is more favorable than in <silcs_fragmap_#2> and if it is positive, then <silcs_fragmap_#2> is more favorable than <silcs_fragmap_#1>.

Note

The difference FragMaps are intended ONLY for visualization and NOT for any quantitative calculations.