Feature quantity calculating method, feature quantity calculating program, and feature quantity calculating device, screening method, screening program, and screening device, compound creating method, compound creating program, and compound creating device
Provided are a feature quantity calculating method, a feature quantity calculating program, and a feature quantity calculating device which enable calculation of a feature quantity accurately showing chemical properties of a target structure, a screening method, a screening program, and a screening device which enable efficient screening of a pharmaceutical candidate compound using a feature quantity, and a compound creating method, a compound creating program, and a compound creating device which enable efficient creation of a three-dimensional structure of a pharmaceutical candidate compound using a feature quantity. Since the chemical properties of target structures are exhibited as the result of an interaction between the target structure and probes in the periphery thereof, the fact that the degree of accumulation of the probes is similar between target structures indicates that the chemical properties of the target structures are similar. Therefore, the feature quantity accurately showing the chemical properties of the target structure can be calculated using the feature quantity calculating method according to one aspect of the present invention.
1. A feature quantity calculating method executed by a computer having a processor, the processor configured to perform the method comprising:
a target structure designating step of designating a target structure formed of a plurality of unit structures having chemical properties;
a three-dimensional structure generating step of generating a three-dimensional structure using the plurality of unit structures for the target structure;
a feature quantity calculating step of calculating a feature quantity obtained by quantifying, in a three-dimensional space, a degree of accumulation of one or more kinds of probes in a periphery of the three-dimensional structure; and
an invariant conversion step of converting the feature quantity into an invariant with respect to rotation and translation of the target structure to calculate an invariant feature quantity,
wherein the probe is a single point having a real electric charge and generating a van der Waals force, and
wherein a compound is designated as the target structure in the target structure designating step,
a three-dimensional structure of the compound formed of a plurality of atoms is generated in the three-dimensional structure generating step,
a first feature quantity which is a feature quantity obtained by quantifying, in the three-dimensional space, the degree of accumulation of the probes in the periphery of the three-dimensional structure of the compound generated in the three-dimensional structure generating step which is the degree of accumulation using one or more kinds of monatomic ions as the probes is calculated in the feature quantity calculating step, and
a first invariant feature quantity is calculated by converting the first feature quantity into an invariant with respect to rotation and translation of the compound in the invariant conversion step.
2. The feature quantity calculating method according to claim 1 ,
wherein the first feature quantity of a first probe that is formed of the one or more kinds of monatomic ions and the first feature quantity of a second probe that is formed of the one or more kinds of monatomic ions and different from the first probe are calculated in the feature quantity calculating step, and
the first invariant feature quantity is calculated using the first feature quantity of the first probe and the first feature quantity of the second probe in the invariant conversion step.
3. A non-temporary computer-readable recording medium which causes a computer to execute the feature quantity calculating method according to claim 1 in a case where a command stored in the recording medium is read by the computer.
4. A screening method executed by a computer having a processor, the processor configured to perform the method of extracting a target compound which is bound to a target biopolymer other than a protein from a plurality of compounds, the method comprising:
a storing step of storing a three-dimensional structure of a compound formed of a plurality of atoms and the first invariant feature quantity of the three-dimensional structure of the compound which is calculated using the feature quantity calculating method according to claim 1 in association with each other for each of the plurality of compounds;
a feature quantity calculating step of calculating the first invariant feature quantity of a binding compound that is a compound whose binding to the target biopolymer other than the protein has been confirmed;
a similarity calculating step of calculating a similarity between the first invariant feature quantity of the plurality of compounds and the first invariant feature quantity of the binding compound; and
a compound extracting step of extracting the target compound from the plurality of compounds based on the similarity.
5. A non-temporary computer-readable recording medium which causes a computer to execute the screening method according to claim 4 in a case where a command stored in the recording medium is read by the computer.
6. A screening device having a processor the processor configured to perform functionality of units, which extracts a target compound bound to a target biopolymer other than a protein from a plurality of compounds, the device comprising:
a storage unit which stores a three-dimensional structure of a compound formed of a plurality of atoms and the first invariant feature quantity of the three-dimensional structure of the compound which is calculated using the feature quantity calculating method according to claim 1 in association with each other for each of the plurality of compounds;
a feature quantity calculation unit which calculates the first invariant feature quantity of a binding compound that is a compound whose binding to the target biopolymer other than the protein has been confirmed;
a similarity calculation unit which calculates a similarity between the first invariant feature quantity of the plurality of compounds and the first invariant feature quantity of the binding compound; and
a compound extraction unit which extracts the target compound from the plurality of compounds based on the similarity.
7. A compound creating method executed by a computer having a processor, the processor configured to perform the method of creating a three-dimensional structure of a target compound that is bound to a target biopolymer other than a protein from a plurality of compounds, the method comprising:
a storing step of storing a three-dimensional structure of a compound formed of a plurality of atoms and the first invariant feature quantity in association with each other for each of the plurality of compounds;
a feature quantity calculating step of calculating the first invariant feature quantity of a binding compound that is a compound whose binding to the target biopolymer other than the protein has been confirmed using the feature quantity calculating method according to claim 1 ;
a generator constructing step of constructing a generator through machine learning using the three-dimensional structure of the plurality of compounds as teacher data and the first invariant feature quantity as an explanatory variable; and
a compound three-dimensional structure generating step of generating a three-dimensional structure of the target compound from the first invariant feature quantity of the binding compound using the generator.
8. A non-temporary computer-readable recording medium which causes a computer to execute the compound creating method according to claim 7 in a case where a command stored in the recording medium is read by the computer.
9. A compound creating device having a processor, the processor is configured to perform functionality of units, which creates a three-dimensional structure of a target compound that is bound to a target biopolymer other than a protein from a plurality of compounds, the device comprising:
a storage unit which stores a three-dimensional structure of a compound formed of a plurality of atoms and a first invariant feature quantity in association with each other for each of the plurality of compounds;
a feature quantity calculation unit which calculates the first invariant feature quantity of a binding compound that is a compound whose binding to the target biopolymer other than the protein has been confirmed using the feature quantity calculating method according to claim 1 ;
a generator construction unit which constructs a generator through machine learning using the three-dimensional structure of the plurality of compounds as teacher data and the first invariant feature quantity as an explanatory variable; and
a compound three-dimensional structure generation unit which generates a three-dimensional structure of the target compound from the first invariant feature quantity of the binding compound using the generator.
10. The feature quantity calculating method according to claim 1 ,
wherein the processor is further configured to designate compounds, indicated by information obtained from an external server and/or an external database via a network, as the target structure.
11. The feature quantity calculating method according to claim 1 ,
wherein the processor is configured to store the invariant feature quantity into a storage device in association with structure information of the target structure.
12. The feature quantity calculating method according to claim 1 ,
wherein the processor is configured to cause a display device to display at least one of the calculated invariant feature quantity and the generated three-dimensional structure.
13. A feature quantity calculating method executed by a computer having a processor, the processor configured to perform the method comprising:
a target structure designating step of designating a target structure formed of a plurality of unit structures having chemical properties;
a three-dimensional structure generating step of generating a three-dimensional structure using the plurality of unit structures for the target structure;
a feature quantity calculating step of calculating a feature quantity obtained by quantifying in a three-dimensional space, a degree of accumulation of one or more kinds of probes in a periphery of the three-dimensional structure; and
an invariant conversion step of converting the feature quantity into an invariant with respect to rotation and translation of the target structure to calculate an invariant feature quantity,
wherein the probe is a single point having a real electric charge and generating a van der Waals force,
wherein a compound is designated as the target structure in the target structure designating step,
a three-dimensional structure of the compound formed of a plurality of atoms is generated in the three-dimensional structure generating step,
a second feature quantity which is a feature quantity obtained by quantifying, in the three-dimensional space, the degree of accumulation of the probes in the periphery of the three-dimensional structure of the compound generated in the three-dimensional structure generating step which is the degree of accumulation using one or more selected from a first point electric charge having an electric charge of + 1 , a second point electric charge having an electric charge of −1, a third point electric charge having an electric charge of +0.1, a fourth point electric charge having an electric charge of −0.1, and a fifth point electric charge having an electric charge of 0, as the probes is calculated in the feature quantity calculating step, and
a second invariant feature quantity is calculated by converting the second feature quantity into an invariant with respect to rotation and translation of the compound in the invariant conversion step.
14. The feature quantity calculating method according to claim 13 ,
wherein the second feature quantity of a first probe that is formed of one or more selected from the first point electric charge, the second point electric charge, the third point electric charge, the fourth point electric charge, and the fifth point electric charge and the second feature quantity of a second probe that is formed of one or more selected from the first point electric charge, the second point electric charge, the third point electric charge, the fourth point electric charge, and the fifth point electric charge and different from the first probe are calculated in the feature quantity calculating step, and
the second invariant feature quantity is calculated using the second feature quantity of the first probe and the second feature quantity of the second probe in the invariant conversion step.
15. The feature quantity calculating method according to claim 14 ,
wherein a compound is designated as the target structure in the target structure designating step,
a three-dimensional structure of the compound formed of a plurality of atoms is generated in the three-dimensional structure generating step,
a third feature quantity which is a feature quantity obtained by quantifying, in the three-dimensional space, the degree of accumulation of the probes in the periphery of the three-dimensional structure of the compound generated in the three-dimensional structure generating step which is the degree of accumulation using the first probe that is formed of one or more kinds of monatomic ions and the second probe that is formed of one or more selected from the first point electric charge having an electric charge of +1, the second point electric charge having an electric charge of −1, the third point electric charge having an electric charge of +0.1, the fourth point electric charge having an electric charge of −0.1, and the fifth point electric charge having an electric charge of 0, as the probes is calculated in the feature quantity calculating step, and
a third invariant feature quantity is calculated using the third feature quantity of the first probe and the third feature quantity of the second probe in the invariant conversion step.
16. The feature quantity calculating method according to claim 15 ,
wherein the third feature quantity of two kinds of the probes in which at least one of the first probe or the second probe is different is calculated in the feature quantity calculating step, and
the third invariant feature quantity is calculated using the third feature quantity of the two kinds of the probes in the invariant conversion step.
17. A screening method executed by a computer having a processor, the processor configured to perform the method of extracting a target compound which is bound to a target biopolymer from a plurality of compounds, the method comprising:
a storing step of storing a three-dimensional structure of a compound formed of a plurality of atoms and the second invariant feature quantity of the three-dimensional structure of the compound which is calculated using the feature quantity calculating method according to claim 4 in association with each other for each of the plurality of compounds;
a feature quantity calculating step of calculating the second invariant feature quantity of a binding compound that is a compound whose binding to the target biopolymer has been confirmed;
a similarity calculating step of calculating a similarity between the second invariant feature quantity of the plurality of compounds and the second invariant feature quantity of the binding compound; and
a compound extracting step of extracting the target compound from the plurality of compounds based on the similarity.
18. A screening device having a processor, the processor configured to perform functionality of units, which extracts a target compound bound to a target biopolymer from a plurality of compounds, the device comprising:
a storage unit which stores a three-dimensional structure of a compound formed of a plurality of atoms and the second invariant feature quantity of the three-dimensional structure of the compound which is calculated using the feature quantity calculating method according to claim 13 in association with each other for each of the plurality of compounds;
a feature quantity calculation unit which calculates the second invariant feature quantity of a binding compound that is a compound whose binding to the target biopolymer has been confirmed;
a similarity calculation unit which calculates a similarity between the second invariant feature quantity of the plurality of compounds and the second invariant feature quantity of the binding compound; and
a compound extraction unit which extracts the target compound from the plurality of compounds based on the similarity.
19. A compound creating method executed by a computer having a processor. the processor configured to perform the method of creating a three-dimensional structure of a target compound that is bound to a target biopolymer from a plurality of compounds, the method comprising:
a storing step of storing a three-dimensional structure of a compound formed of a plurality of atoms and a second invariant feature quantity in association with each other for each of the plurality of compounds;
a feature quantity calculating step of calculating the second invariant feature quantity of a binding compound that is a compound whose binding to the target biopolymer has been confirmed using the feature quantity calculating method according to claim 13 ;
a generator constructing step of constructing a generator through machine learning using the three-dimensional structure of the plurality of compounds as teacher data and the second invariant feature quantity as an explanatory variable; and
a compound three-dimensional structure generating step of generating a three-dimensional structure of the target compound from the second invariant feature quantity of the binding compound using the generator.
20. A compound creating device having a processor, the processor configured to perform functionality of units which creates a three-dimensional structure of a target compound that is bound to a target biopolymer from a plurality of compounds, the device comprising:
a storage unit which stores a three-dimensional structure of a compound formed of a plurality of atoms and a second invariant feature quantity in association with each other for each of the plurality of compounds;
a feature quantity calculation unit which calculates the second invariant feature quantity of a binding compound that is a compound whose binding to the target biopolymer has been confirmed using the feature quantity calculating method according to claim 13 ;
a generator construction unit which constructs a generator through machine learning using the three-dimensional structure of the plurality of compounds as teacher data and the second invariant feature quantity as an explanatory variable; and
a compound three-dimensional structure generation unit which generates a three-dimensional structure of the target compound from the second invariant feature quantity of the binding compound using the generator.
21. A feature quantity calculating device having a processor, the processor configured to perform functionality of units, comprising:
a target structure designation unit which designates a target structure formed of a plurality of unit structures having chemical properties;
a three-dimensional structure generation unit which generates a three-dimensional structure using the plurality of unit structures for the target structure;
a feature quantity calculation unit which calculates a feature quantity obtained by quantifying, in a three-dimensional space, a degree of accumulation of one or more kinds of probes in a periphery of the three-dimensional structure; and
an invariant conversion unit which converts the feature quantity into an invariant with respect to rotation and translation of the target structure to calculate an invariant feature quantity,
wherein the probe is a single point having a real electric charge and generating a van der Waals force, and
wherein a compound is designated as the target structure in the target structure designating step
a three-dimensional structure of the compound formed of a plurality of atoms is generated in the three-dimensional structure generating step,
a first feature quantity which is a feature quantity obtained by quantifying, in the three-dimensional space, the degree of accumulation of the probes in the periphery of the three-dimensional structure of the compound generated in the three-dimensional structure generating step which is the degree of accumulation using one or more kinds of monatomic ions as the probes is calculated in the feature quantity calculating step, and
a first invariant feature quantity is calculated by converting the first feature quantity into an invariant with respect to rotation and translation of the compound in the invariant conversion step.
22. The feature quantity calculating device according to claim 21 ,
wherein the processor is further configured to designate compounds, indicated by information obtained from an external server and/or an external database via a network, as the target structure.
23. The feature quantity calculating device according to claim 21 ,
wherein the processor is configured to store the invariant feature quantity into a storage device in association with structure information of the target structure.
24. The feature quantity calculating device according to claim 21 ,
wherein the processor is configured to cause a display device to display at least one of the calculated invariant feature quantity and the generated three-dimensional structure.