Computational Method to Identify Protein Hotspots and Allosteric Sites

A system for characterizing a protein comprising:

• a non-transitory computer-readable medium having stored thereon instructions that, when executed by a processor, cause the processor to:
• a) access simulated protein structure data, wherein the simulated protein structure data indicate a structure of the protein;
• b) cluster the simulated protein structure data to produce a plurality of clustered structures and determine an equilibrium of each clustered structure in the plurality of clustered structures;
• c) calculate time-dependent responses of each clustered structure in the plurality of clustered structures;
• d) identify at least one residue of interest based on the time-dependent responses of each clustered structure in the plurality of clustered structures;
• and
• e) characterize the at least one residue of interest and the protein.

A non-transitory computer-readable medium having stored thereon instructions that, when executed by a processor to:

• a) access simulated protein structure data, wherein the simulated protein structure data indicate a structure of the protein;
• b) cluster the simulated protein structure data to produce a plurality of clustered structures and determine an equilibrium of each clustered structure in the plurality of clustered structures;
• c) calculate time-dependent responses of each clustered structure in the plurality of clustered structures;
• d) identify at least one residue of interest based on the time-dependent responses of each clustered structure in the plurality of clustered structures;
• and
• e) characterize the at least one residue of interest and the protein.