公开(公告)号：EP4020483A1

公开(公告)日：2022-06-29

申请号：EP21202111.7

申请日：2021-10-12

申请人： FUJITSU LIMITED

发明人： Tanida, Yoshiaki

IPC分类号： G16B15/30 ,  C07K7/00 ,  G16C20/50

摘要： A stable structure search method for a computer to execute a process includes determining an initial structure of a trans-type cyclic peptide so that all of dihedral angles between a carbon atom and a nitrogen atom that form a peptide bond in the trans-type cyclic peptide are from 150° to 210°; and perform a first molecular simulation of a structure of the trans-type cyclic peptide by using the initial structure.

公开(公告)号：EP2509015A2

公开(公告)日：2012-10-10

申请号：EP12152740.2

申请日：2012-01-26

申请人： Fujitsu Limited

发明人： Tanida, Yoshiaki

IPC分类号： G06F19/00

CPC分类号： G06F19/701 ,  G06F19/16 ,  G06F19/704 ,  G06F19/706

摘要： In a free energy difference estimation method, the partial free energy difference indicates a bound state between a target compound and a first candidate compound bindable to the target compound, and is stored in a storage part for each value of a binding constant. A change region, in which a partial free energy difference is equal to or greater than a predetermined change value, is specified in a region of the binding constant. The partial free energy difference of a second candidate compound in the change region is interpolated based on the partial free energy difference acquired in each of a previous region and a following region by using an approximation function.

摘要翻译： 在自由能差估计方法中，部分自由能差表示目标化合物与能够与目标化合物结合的第一候选化合物之间的结合状态，并且存储在结合常数的每个值的存储部分中。 在结合常数的区域中指定其中部分自由能差等于或大于预定变化值的变化区域。 基于通过使用近似函数在先前区域和后续区域中的每一个中获取的部分自由能差异来内插变化区域中的第二候选化合物的部分自由能差异。

公开(公告)号：EP4156193A1

公开(公告)日：2023-03-29

申请号：EP22174824.7

申请日：2022-05-23

申请人： FUJITSU LIMITED

发明人： Tanida, Yoshiaki

IPC分类号： G16B15/20 ,  G16B15/30

摘要： An initial conformation generation apparatus includes a generation unit that generates a model representing a cyclic peptide molecule by identifying Cα atoms of each of a plurality of amino acid residues, by arranging the identified Cα atoms on a circumference, and by adding main chains and side chains of the plurality of amino acid residues; and a search instruction unit that causes a search unit to search for a stable conformation of the cyclic peptide molecule by using the generated model as an initial conformation of the cyclic peptide molecule.

公开(公告)号：EP4102510A1

公开(公告)日：2022-12-14

申请号：EP22159683.6

申请日：2022-03-02

申请人： FUJITSU LIMITED

发明人： Terashima, Chieko ,  Tanida, Yoshiaki ,  Sato, Hiroyuki

IPC分类号： G16C20/40

摘要： A stable structure search system includes a calculation unit that acquires a plurality of degrees of structure similarity between each of a plurality of kinds of molecules and a first molecule included in a target molecule based on each interaction potential of the plurality of kinds of molecules, acquires a plurality of degrees of charge similarity between each of the plurality of kinds of molecules and the first molecule, and acquires a plurality of total degrees of similarity based on sums of each of the plurality of degrees of structure similarity and each of the plurality of degrees of charge similarity; and an identification unit that determines a second molecule whose total degree of similarly is largest among the plurality of kinds of molecules, acquires energy of a molecular structure of the target molecule based on an interaction potential of the second molecule.

公开(公告)号：EP2782033A1

公开(公告)日：2014-09-24

申请号：EP14152546.9

申请日：2014-01-24

申请人： FUJITSU LIMITED

发明人： Tanida, Yoshiaki

IPC分类号： G06F19/00 ,  G06F19/16

CPC分类号： G06F19/12 ,  G06F19/16 ,  G06F19/706

摘要： A calculation method of binding free energy, which includes: calculating solvation energy (ΔG 1 ) between a solvent and a compound; and calculating an energy change (ΔG 2 ) between a bound state (λ=0) where the compound and a protein are bound, and an unbound state (λ=1) where the compound and the protein are not bound, wherein the calculating the energy change (ΔG 2 ) includes: determining a distance (D th ), within which structure sampling is performed; calculating a change in binding energy (ΔG 21 ) between the compound and the protein within a distance equal to or shorter than the distance (D th ), calculating a change in solvation energy (ΔG 23 ) between the solvent and the compound with ignoring an influence of the protein, calculating a change in binding energy (ΔG 22 ) between the compound and the protein with interpolation, and calculating a correction term (ΔG 24 ) with respect to a standard state.

摘要翻译： 结合自由能的计算方法，包括：溶剂和化合物之间计算的溶剂化能量（“G 1）; 以及计算上，其中该化合物和蛋白质结合“（= 0）处于束缚态之间（G 2能量变化）”，并且，其中所述化合物和所述蛋白不结合，worin计算未结合状态（“= 1） 的能量变化（“G 2）包括：确定性采矿的距离（D th）时，在其内结构采样被执行; 在“化合物和比距离（D th）的等于或短的距离内的蛋白之间（G 21，计算在溶剂化能的变化结合能）中的溶剂并与化合物之间（” G 23）计算的变化 忽略的蛋白质的影响，计算结合能的变化（下称“化合物和蛋白之间与插补G 22），并计算校正项相对于（” G 24）为标准状态。

公开(公告)号：EP4250303A1

公开(公告)日：2023-09-27

申请号：EP22217113.4

申请日：2022-12-29

申请人： FUJITSU LIMITED

发明人： Manabe, Toshio ,  Sato, Hiroyuki ,  Tanida, Yoshiaki ,  Terashima, Chieko

IPC分类号： G16C20/30 ,  G16C20/40 ,  G16B15/00

摘要： A search program comprising instructions which, when executed by a computer, cause the computer to execute processing including: obtaining a first cost value of a first potential that corresponds to interaction between coarse-grained particles, a second cost value of a second potential that corresponds to an angle and a dihedral angle between the particles, and a third cost value of a third potential that corresponds to repulsion and attraction between the particles; and instructing an Ising apparatus to search for a structure of a coarse-grained model with which a total sum of the first cost value, the second cost value, and the third cost value calculated for an entirety of the coarse-grained model that includes a plurality of particles satisfies a predetermined condition.

公开(公告)号：EP2509015A3

公开(公告)日：2016-03-02

申请号：EP12152740.2

申请日：2012-01-26

申请人： Fujitsu Limited

发明人： Tanida, Yoshiaki

IPC分类号： G06F19/00 ,  G06F19/16

CPC分类号： G06F19/701 ,  G06F19/16 ,  G06F19/704 ,  G06F19/706

摘要： In a free energy difference estimation method, the partial free energy difference indicates a bound state between a target compound and a first candidate compound bindable to the target compound, and is stored in a storage part for each value of a binding constant. A change region, in which a partial free energy difference is equal to or greater than a predetermined change value, is specified in a region of the binding constant. The partial free energy difference of a second candidate compound in the change region is interpolated based on the partial free energy difference acquired in each of a previous region and a following region by using an approximation function.