Compound docking calculation processing device, compound docking calculation processing method, and program

A compound docking calculation processing method, comprising:

• a fragment decomposition step of acquiring fragment data indicating fragments, which are chemical substructures of a compound used to perform docking calculation with a target biomolecule;
• a fragment docking calculation step of executing, for each fragment indicated by the fragment data, fragment docking calculation between the fragment and the target biomolecule;
• a fragment interaction evaluation step of calculating, based on the result of fragment docking calculation for each fragment placement candidate which is a placement candidate when the fragment binds to the target biomolecule and a positional relationship between the fragment placement candidates, evaluation values for the fragment placement candidates and the interrelationship between the fragment placement candidates;
• an evaluation function generation step of generating an evaluation function of giving an evaluation value for a fragment pose set of the fragments constituting the compound on the surface of the target biomolecule based on the evaluation value;
• and
• a combinatorial optimization calculation processing step of calculating a fragment pose set of the fragments constituting the compound on the surface of the target biomolecule by determining a state that optimizes the evaluation function based on combinatorial optimization.

A program causing a computer to execute:

• a fragment decomposition step of acquiring fragment data indicating fragments, which are chemical substructures of a compound used to perform docking calculation with a target biomolecule;
• a fragment docking calculation step of executing, for each fragment indicated by the fragment data, fragment docking calculation between the fragment and the target biomolecule;
• a fragment interaction evaluation step of calculating, based on the result of fragment docking calculation for each fragment placement candidate which is a placement candidate when the fragment binds to the target biomolecule and a positional relationship between the fragment placement candidates, evaluation values for the fragment placement candidates and the interrelationship between the fragment placement candidate;
• an evaluation function generation step of generating an evaluation function of giving an evaluation value for a fragment pose set of the fragments constituting the compound on the surface of the target biomolecule based on the evaluation value;
• and
• a combinatorial optimization calculation processing step of calculating a fragment pose set of the fragments constituting the compound on the surface of the target biomolecule by determining a state that optimizes the evaluation function based on combinatorial optimization.