DEVICE AND METHOD FOR SEARCHING COMPOUND

• US 20200135295A1
• Filed: 09/11/2019
• Published: 04/30/2020
• Est. Priority Date: 10/26/2018
• Status: Active Application

• Current Assignee: Fujitsu Limited
• Original Assignee: Fujitsu Limited
• Inventors: Shibasaki, Takayuki, Uemura, Taiki
• Application Number:
  US16/567,294
• Publication Number:
  US 20200135295A1
• Time in Patent Office: Days
• CPC Class Codes: G16B 15/10 Nucleic acid folding
• CPC Class Codes: G16B 15/20 Protein or domain folding
• CPC Class Codes: G16B 50/30 Data warehousing; Computing architectures

Abstract

A device including: a defining unit to define lattice space that is collection of lattices where compound groups are sequentially arranged; a limiting unit; an assigning unit; an arithmetic unit; a judging unit; and a controlling unit to cause the limiting unit to execute expansion of the limited lattice space, the assigning unit to execute assignment of the bits to the lattice points included in the limited lattice space after the expansion, and the arithmetic unit to execute calculation of the minimum energy, in case where the judging unit judges any of the compound groups assigned to the lattice points is arranged on the outermost edge, wherein the device is device for searching the compound, in which the compound groups are linked with one another.

Claims

1. A device for searching a compound, comprising:

a defining unit configured to define a lattice space that is a collection of lattices where a plurality of compound groups are sequentially arranged;

a limiting unit configured to, in a case where any of the compound groups is arranged in any of the lattices of the lattice space, followed by arranging a next compound group in the lattice space, generate a limited lattice space that is a space created by eliminating, from the lattice space, undesirable regions for the next compound group to be arranged;

an assigning unit configured to assign a bit to each of lattice points, to which the compound groups can be arranged, in the limited lattice space;

an arithmetic unit configured to perform a ground state search on an Ising model obtained through conversion based on restriction conditions related to each of the lattice points according to simulated annealing, to thereby calculate minimum energy of the Ising model;

a judging unit configured to judge whether any of the compound groups assigned to the lattice points is arranged on an outermost edge of the limited lattice space or not; and

a controlling unit configured to cause the limiting unit to execute expansion of the limited lattice space, cause the assigning unit to execute assignment of the bits to the lattice points included in the limited lattice space after the expansion, and cause the arithmetic unit to execute calculation of the minimum energy of the Ising model, in a case where the judging unit judges that any of the compound groups assigned to the lattice points is arranged on the outermost edge of the limited lattice space,

wherein the device is a device for searching the compound, in which a plurality of the compound groups are linked with one another.

2. The device according to claim 1,

wherein the judging unit is configured to judge whether any of the compound groups excluding the compound group arranged first and the compound group arranged last is arranged on the outermost edge of the limited lattice space among the compound groups assigned to the lattice points.

3. The device according to claim 1,

wherein the controlling unit is configured to cause the limiting unit to execute expansion of the limited lattice space based on expansion information.

4. The device according to claim 1,

wherein the controlling unit is configured not to change the bits already assigned to the lattice points of the compound group judged as being arranged on the outermost edge of the limited lattice space and the compound groups arranged earlier than the compound group judged as being arranged on the outermost edge of the limited lattice space.

5. The device according to claim 1,

wherein the controlling unit is configured to expand only a lattice space surrounding the compound group arranged on the outermost edge of the limited lattice space when the controlling unit causes the limiting unit to execute expansion of the limited lattice space.

6. The device according to claim 3,

wherein the expansion information considers a difference (n−

M) between the order (n) of the arrangement of a compound group arranged last, and the order (M) of arrangement of the compound group judged as being arranged on the outermost edge of the limited lattice space, and

the controlling unit is configured to cause the limiting unit to execute expansion of the limited lattice space based on the expansion information in a manner that the limited lattice space is expanded smaller when the difference (n−

M) is small than when the difference (n−

M) is large.

7. The device according to claim 1,

wherein the compound groups are amino acid residues.

8. The device according to claim 7,

wherein the compound is a protein.

9. A method for searching a compound, the method comprising:

defining a lattice space that is a collection of lattices where a plurality of compound groups are sequentially arranged;

in a case where any of the compound groups is arranged in any of the lattices of the lattice space, followed by arranging a next compound group in the lattice space, generating a limited lattice space that is a space created by eliminating, from the lattice space, undesirable regions for the next compound group to be arranged;

assigning a bit to each of lattice points, to which the compound groups can be arranged, in the limited lattice space;

performing a ground state search on an Ising model obtained through conversion based on restriction conditions related to each of the lattice points according to simulated annealing, to thereby calculate minimum energy of the Ising model;

judging whether any of the compound groups assigned to the lattice points is arranged on the outermost edge of the limited lattice space or not; and

executing expansion of the limited lattice space, assignment of the bits to the lattice points included in the limited lattice space after the expansion, and calculation of the minimum energy of an Ising model, in a case where it is judged that any of the compound groups assigned to the lattice points is arranged on the outermost edge of the limited lattice space,

wherein the method is a method for allowing a computer to search the compound in which a plurality of the compound groups are linked with one another.

10. The method according to claim 9,

wherein the judging is judging whether any of the compound groups excluding the compound group arranged first and the compound group arranged last is arranged on the outermost edge of the limited lattice space among the compound groups assigned to the lattice points.

11. The method according to claim 9,

wherein the expanding is expanding the limited lattice space based on expansion information.

12. The method according to claim 9,

wherein the bits already assigned to the lattice points of the compound group judged as being arranged on the outermost edge of the limited lattice space and the compound groups arranged earlier than the compound group judged as being arranged on the outermost edge of the limited lattice space are not changed.

13. The method according to claim 9,

wherein, in the expansion of the limited lattice space, only a lattice space surrounding the compound group arranged on the outermost edge of the limited lattice space is expanded.

14. The method according to claim 11,

wherein the expansion information considers a difference (n−

M) between the order (n) of the arrangement of a compound group arranged last, and the order (M) of arrangement of the compound group judged as being arranged on the outermost edge of the limited lattice space, and

the expansion is expanding the limited lattice space based on the expansion information in a manner that the limited lattice space is expanded smaller when the difference (n−

M) is small than when the difference (n−

M) is large.

15. The method according to claim 9,

wherein the compound groups are amino acid residues.

16. The method according to claim 15,

wherein the compound is a protein.