Multipole moment based coarse grained representation of antibody electrostatics

A system comprising:

• one or more data processors;
• and
• a non-transitory, computer-readable storage medium containing instructions which, when executed on the one or more data processors, cause the one or more data processors to perform actions including:
• ascertaining a plurality of molecular multipole moments of an antibody molecule;
• creating a model of the antibody molecule by selecting a plurality of sites within a representation of the antibody molecule, wherein:
• a total number of the plurality of sites is less than a total number of atoms in the antibody molecule;
• the plurality of sites comprises a first subset of the plurality of sites and a second subset of the plurality of sites;
• and
• a total number of sites within the first subset of the plurality of sites is equal to a total number of molecular multipole moments within the plurality of molecular multipole moments;
• calculating a charge for each of the plurality of sites, wherein:
• a combination of calculated charges for the plurality of sites approximates the plurality of molecular multipole moments of the antibody molecule;
• and
• for each site of the second subset of the plurality of sites, a charge calculated for each site is equal to a charge calculated for a corresponding site of the first subset of the plurality of sites;
• executing a molecular dynamics simulation representing a plurality of molecules in a solution to generate a time-dependent trajectory data for the model of the antibody molecule, wherein at least one molecule of the plurality of molecules is an instance of the model of the antibody molecule and the molecular dynamics simulation simulates interactions based on the charges calculated for each of the plurality of sites within the representation of the antibody molecule;
• predicting a property of the solution using data from the molecular dynamics simulation;
• and
• outputting the predicted property of the solution.

A computer-program product tangibly embodied in a non-transitory machine-readable storage medium, including instructions configured to cause one or more data processors to perform actions including:

• ascertaining a plurality of molecular multipole moments of an antibody molecule;
• creating a model of the antibody molecule by selecting a plurality of sites within a representation of the antibody molecule, wherein:
• a total number of the plurality of sites is less than a total number of atoms in the antibody molecule;
• the plurality of sites comprises a first subset of the plurality of sites and a second subset of the plurality of sites;
• and
• a total number of sites within the first subset of the plurality of sites is equal to a total number of molecular multipole moments within the plurality of molecular multipole moments;
• calculating a charge for each of the plurality of sites, wherein:
• a combination of calculated charges for the plurality of sites approximates the plurality of molecular multipole moments of the antibody molecule;
• and
• for each site of the second subset of the plurality of sites, a charge calculated for each site is equal to a charge calculated for a corresponding site of the first subset of the plurality of sites;
• executing a molecular dynamics simulation representing a plurality of molecules in a solution to generate a time-dependent trajectory data for the model of the antibody molecule, wherein at least one molecule of the plurality of molecules is an instance of the model of the antibody molecule and the molecular dynamics simulation simulates interactions based on the charges calculated for each of the plurality of sites within the representation of the antibody molecule;
• predicting a property of the solution using data from the molecular dynamics simulation;
• and
• outputting the predicted property of the solution.