KR102199500B1 - A three dimensional image generation appratus of amino acid residues in protein context and thereof method - Google Patents

Abstract

, N, C의 원자를 3차원의 공간 좌표에 표시하는 공간좌표 표시부, 그리고 상기 3차원 공간 좌표에 상기 그룹을 형성하는 모든 원자들을 표시하는 3차원 이미지 변환부를 포함 포함한다.
이와 같이 본 발명에 따르면, 단백질의 아미노산 잔기와 그 주변환경을 표현하는 3차원 이미지를 생성함으로써 데이터 분석 및 인공지능 모델을 학습 할 수 있는 데이터로 사용할 수 있으므로 인공지능 융합의 새로운 가능성을 열어줄 원료로 제공될 수 있는 효과를 지닌다. The present invention relates to an apparatus and method for generating a three-dimensional image of an environment around an amino acid residue of a protein.
According to the present invention, a protein data input unit that receives structural data for a protein, calculates the distance between atoms included in each residue constituting the protein using the input protein structure data, and uses the calculated distance value. A group-forming part forming a group for a residue, included in the formed group, which is the basic constitution of each residue

, A spatial coordinate display unit that displays N, C atoms in three-dimensional spatial coordinates, and a three-dimensional image conversion unit that displays all the atoms forming the group in the three-dimensional spatial coordinates.
As described above, according to the present invention, it can be used as data for learning data analysis and artificial intelligence models by creating a three-dimensional image representing the amino acid residues of proteins and their surroundings, thus opening up new possibilities for artificial intelligence fusion. It has an effect that can be provided as

Description

A three dimensional image generation appratus of amino acid residues in protein context and thereof method

The present invention relates to an apparatus and method for generating a three-dimensional image of an environment around amino acid residues of a protein, and more particularly, to an amino acid residue of a protein for generating data in the form of a three-dimensional image of amino acid residues and its surrounding environment. It relates to an apparatus and a method for generating a 3D image of a surrounding environment.

The pharmaceutical bio industry is paying high attention to artificial intelligence convergence in order to reduce the cost of research and development of new drugs and lower the failure rate in clinical trials, and big data analysis through artificial intelligence will bring innovation in all stages and development processes of new drugs. Expected.

In order to train an artificial intelligence model, chemical and biological big data is required. Representative big data includes PDB (Protein Data Bank). PDB is a protein database operated by Brookhaven National Laboratory in the United States, a place that collects information on the tertiary structures of macromolecules in vivo discovered through experiments. Therefore, PDB provides information on atomic coordinates, bibliographic citations, primary and secondary structure information, crystallographic structures, and the like.

Recently, the pharmaceutical bio industry is also producing various feature data due to the increasing need for artificial intelligence fusion, and image data applicable to convolutional neural networks emerging in the field of artificial intelligence such as deep learning. There is an increasing need for

The technology behind the present invention is disclosed in Korean Patent Application Publication No. 10-2001-0020443 (published on 15 March 2001).

It is an object of the present invention to provide an apparatus and method for generating a three-dimensional image of an environment around amino acid residues of a protein that generates amino acid residues of a protein and its surrounding environment as data in the form of a three-dimensional image. .

, N, C의 원자를 3차원의 공간 좌표에 표시하는 공간좌표 표시부, 그리고 상기 3차원 공간 좌표에 상기 그룹을 형성하는 모든 원자들을 표시하는 3차원 이미지 변환부를 포함한다. According to an embodiment of the present invention for achieving such a technical problem, in an apparatus for generating a three-dimensional image of an environment around an amino acid residue of a protein, a protein data input unit receiving structural data for a protein, and the input protein structure data A group forming part that forms a group for residues by calculating the distance between atoms included in each residue constituting the protein, and using the calculated distance value, included in the formed group, and the basic composition of each residue Become

, A spatial coordinate display unit displaying atoms of N, C in three-dimensional spatial coordinates, and a three-dimensional image conversion unit displaying all atoms forming the group in the three-dimensional spatial coordinates.

The group forming unit decomposes for each residue using the received protein structure data, calculates the distance between all atoms included in the decomposed residue, and then sets a preset centering on a specific atom included in the corresponding residue. It is possible to obtain and group information on all atoms located within a radius having a cutoff value.

All the atoms to be grouped may include atoms included in the corresponding residue with the center point and atoms of other residues located within the set radius.

, N, C의 원자에 대한 정보를 획득하는 원자 정보 획득모듈, 그리고 상기 백본에서 획득한

, N, C의 원자가 이루는 평면이 3차원의 공간좌표의 XY축의 평면과 평행이 되도록 위치시키고, 상기 XY축과 평행하게 위치한

, N, C의 원자 중에서

을 원점에 위치시킨 다음, 상기

을 중심으로 N과 C를 좌표변환 및 회전처리를 이용하여 정규화하는 공간좌표 표준화 모듈을 포함할 수 있다. The spatial coordinate display unit distinguishes whether the grouped residue is glycine (GLY), is located in the protein backbone, and all residues have the same

, Atomic information acquisition module that acquires information on the atoms of N, C, and obtained from the backbone

, The plane formed by the atoms of N, C is positioned so that it is parallel to the plane of the XY axis of the three-dimensional spatial coordinates, and is located parallel to the XY axis.

, Among the atoms of N, C

To the origin, and then

It may include a spatial coordinate standardization module that normalizes N and C by using coordinate transformation and rotation processing around.

의 좌표가 XY축의 원점에 위치하도록 좌표를 이동시키고, 상기

을 원점에 위치시킨 상태에서 N의 좌표를 XY축의 평면에 사영시킨 다음, XY축의 평면에 위치한 N의 좌표에 대한

벡터와 Y축의 사이에 형성된 사잇각을 이용하여 N의 좌표가 YZ축의 평면에 닿도록 Z축을 회전시키며, 상기 회전된 N의 좌표에 대한

벡터와 Y축의 사이에 형성된 사잇각을 이용하여 N의 좌표가 XY축의 평면에 닿도록 X축을 회전시키고, 그리고 상기 C의 좌표를 XZ축의 평면에 사영시킨 다음,

벡터와 X축의 사이에 형성된 사잇각을 이용하여 C의 좌표가 XY축의 평면에 닿도록 Y축을 회전시킴으로써, 상기

, N, C의 원자가 XY축의 평면상에 평행하게 위치시킬 수 있다. The spatial coordinate standardization module, among the three atoms

Move the coordinates so that the coordinates of are located at the origin of the XY axis, and

Position N at the origin, project the coordinates of N onto the plane of the XY axis, and then project the coordinates of N at the plane of the XY axis.

The Z axis is rotated so that the coordinates of N touch the plane of the YZ axis by using the angle formed between the vector and the Y axis, and

The X axis is rotated so that the coordinates of N touch the plane of the XY axis by using the angle formed between the vector and the Y axis, and the coordinates of C are projected onto the plane of the XZ axis,

By rotating the Y-axis so that the coordinates of C touch the plane of the XY-axis by using the angle formed between the vector and the X-axis, the above

, N, C atoms can be positioned parallel to the plane of the XY axis.

의 좌표를 원점에 위치시킨 상태에서

벡터는 y축과 평행하고, C의 좌표는

와 N의 좌표보다 큰 위치값을 가질 수 있다. The spatial coordinate standardization module, the

With the coordinates of

The vector is parallel to the y-axis, and the coordinates of C are

It can have a position value greater than the coordinates of and N.

, N, C의 좌표를 잔기의

가 원점이 되는 좌표에 이동하여 위치시킨 다음, 상기

를 중심으로 상기

와의 거리가 컷오프(cutoff)값보다 작은 모든 원자의 좌표를 표시할 수 있다. The three-dimensional image conversion unit is normalized on the plane of the XY axis

, N, C coordinates of the residues

Move to the coordinate where is the origin and place it, then

Centered on

It is possible to display the coordinates of all atoms whose distance to is less than the cutoff value.

, N, C의 좌표의

를 중심으로 상기

와의 거리가 컷오프(cutoff)값보다 작은 모든 원자의 좌표를 표시할 수 있다. The 3D image conversion unit, when the grouped residue is glycine (GLY), normalized on the plane of the XY axis

, N, C of the coordinates

Centered on

It is possible to display the coordinates of all atoms whose distance to is less than the cutoff value.

, N, C의 원자를 3차원의 공간 좌표로 정규화하는 단계, 그리고 상기 3차원 공간 좌표에 상기 그룹을 형성하는 모든 원자들을 표시하여 이미지화하는 단계를 포함한다. In addition, according to an embodiment of the present invention, in a method of generating a three-dimensional image of an environment around an amino acid residue of a protein using a three-dimensional image generating device, receiving structural data for a protein, using the input protein structure data By calculating the distance between atoms included in each residue constituting the protein, and forming a group for the residue using the calculated distance value, which is included in the formed group and becomes the basic constitution of each residue.

, Normalizing the atoms of N, C to three-dimensional spatial coordinates, and displaying and imaged all the atoms forming the group in the three-dimensional spatial coordinates.

As described above, according to the present invention, a three-dimensional image representing the amino acid residues of a protein and its surroundings can be generated and used as data for data analysis and learning of artificial intelligence models, thus opening up new possibilities for artificial intelligence fusion. It has an effect that can be provided as

In addition, according to the present invention, since the process of normalizing to the same position line when performing 3D image generation, it is possible to effectively identify the kind of residue and contact with other residues, and through hydrogen removal and channel increase, etc. It is possible to achieve an effect that can be expanded into a desired shape.

1 is a block diagram showing a 3D image generating apparatus according to an embodiment of the present invention.
FIG. 2 is a diagram schematically illustrating a spatial coordinate display unit shown in FIG. 1.
3 is a flowchart schematically illustrating a method of generating a 3D image using a 3D image generating apparatus according to an embodiment of the present invention.
4 is an exemplary view showing a state in which the protein is decomposed by residues in step S320 shown in FIG. 3.
5 is a flowchart schematically illustrating step S330 shown in FIG. 3.
6 is a flowchart schematically illustrating step S340 illustrated in FIG. 3.
FIG. 7 is an exemplary diagram schematically showing a method of positioning N on the plane of the YZ axis in step S344 shown in FIG. 6.
FIG. 8 is an exemplary diagram schematically showing a method of normalizing by placing N on a plane of the XY axis in step S345 shown in FIG. 6.
9 is an exemplary view schematically showing a method of normalizing by placing a C atom on a plane of the XY axis in step S346 shown in FIG. 6.
FIG. 10 is an exemplary view showing a state in which all elements grouped in step S350 shown in FIG. 3 are displayed in a three-dimensional coordinate space.

Hereinafter, preferred embodiments of the present invention will be described in detail with reference to the accompanying drawings. In this process, the thickness of the lines or the size of components shown in the drawings may be exaggerated for clarity and convenience of description.

In addition, terms to be described later are terms defined in consideration of functions in the present invention, which may vary according to the intention or custom of users or operators. Therefore, definitions of these terms should be made based on the contents throughout the present specification.

Hereinafter, an apparatus for generating a 3D image according to an embodiment of the present invention will be described with reference to FIGS. 1 and 2.

1 is a block diagram showing a 3D image generating apparatus according to an embodiment of the present invention.

As shown in FIG. 1, the 3D image generating apparatus 100 according to the embodiment of the present invention includes a protein data input unit 110, a group forming unit 120, a spatial coordinate display unit 130, and a 3D image conversion unit ( 140).

First, the protein data input unit 110 receives structural data for a protein. In this case, the protein structure data is in the form of a pdb file, and includes information on coordinates on a three-dimensional orthogonal coordinate for amino acids contained in the protein.

The group forming unit 120 decomposes each residue by using the input protein structure data, and calculates a distance value between atoms included in the residue. Then, the group forming unit 120 uses the distance value to form a group of all atoms located within a predetermined radius from the atom serving as the center of the residue.

In other words, proteins contain dozens to thousands of amino acids, or residues, and residues are made up of a plurality of atoms. Accordingly, the group forming unit 120 decomposes by residue, and calculates a distance value between atoms constituting the residue by using atomic coordinates included in the protein structure data. Then, the group forming unit 120 forms a group for all atoms located within a certain radius from the central point or the central atom located inside the residue. That is, the group formed by the group forming unit 120 may include elements of residues and other residues located around them.

, N, C의 원자를 3차원의 공간 좌표상에 표시 표시하며, 백본에 포함된

, N, C의 원자에 대한 정규화를 수행한다. The spatial coordinate display unit 130 corresponds to a backbone of a residue among grouped atoms.

, N, C atoms are displayed on three-dimensional spatial coordinates, and included in the backbone.

, N, C performs normalization on the atoms.

, N, C의 원자를 중심으로 그룹형성부(120)에서 그룹화한 모든 원자들을 3차원 공간좌표에 표시한다. The 3D image conversion unit 140

All the atoms grouped by the group forming unit 120 centering on the atoms of, N, and C are displayed on the three-dimensional spatial coordinates.

FIG. 2 is a diagram schematically illustrating a spatial coordinate display unit shown in FIG. 1.

As shown in FIG. 2, the spatial coordinate display unit 130 includes an atomic information acquisition module 131 and a spatial coordinate standardization module 132.

, N, C의 원자에 대한 정보를 획득한다. First, the atomic information acquisition module 131 is located in the protein backbone and all residues have the same

, N, C to obtain information on the atoms.

, N, C의 원자가 이루는 평면이 3차원의 공간좌표의 XY축의 평면과 평행이 되도록 위치시킨다. 그 다음, 공간좌표 표준화 모듈(132)은 XY축과 평행하게 위치한

, N, C의 원자를 순서대로 좌표변환 및 회전 처리하여,

, N, C의 원자를 XY평면의 동일한 위치선상에 정규화시킨다. And, the spatial coordinate standardization module 132 uses the information acquired from the backbone

, N and C atoms are positioned so that the plane is parallel to the plane of the XY axis of the three-dimensional spatial coordinates. Then, the spatial coordinate standardization module 132 is located parallel to the XY axis.

, N, C atoms in order by coordinate transformation and rotation processing,

, N, C atoms are normalized on the same position line in the XY plane.

Hereinafter, a method for generating a 3D image using a 3D image generating apparatus according to an embodiment of the present invention will be described in more detail with reference to FIGS. 3 and 10.

3 is a flowchart schematically illustrating a method of generating a 3D image using a 3D image generating apparatus according to an embodiment of the present invention.

As shown in FIG. 3, first, the protein data input unit 110 receives structural data for a protein from an external server (S310).

In other words, the protein data input unit 110 receives protein data including information on atomic coordinates from a Protein Data Bank (PDB). At this time, the Protein Data Bank (PDB) provides protein data in the form of a PDB file.

Then, the group forming unit 120 decomposes the protein for each residue by using the structure information included in the received protein structure data (S320).

4 is an exemplary view showing a state in which the protein is decomposed by residues in step S320 shown in FIG. 3.

, N, C를 중심으로 잔기를 분해한다.As shown in FIG. 4, the group forming part 120 corresponds to the backbone of the protein and becomes the basic constitution of the residue.

, N, C to decompose the residue.

)와 질소(N) 및 탄소(C)를 중심으로 수소(H), 산소(O) 또는 다른 사이드 체인을 포함한다. 따라서, 그룹형성부(120)는 아미노산 즉, 잔기마다 기본 원자로 포함되는 알파탄소(

)와 질소(N) 및 탄소(C)를 중심으로 단백질을 잔기별로 분해한다. First, when describing amino acids, amino acids refer to molecules having a specific structure in which an amine group having a basic property (-NH2) and a carboxyl group having an acidic property (-COOH) coexist. The amine and carboxyl groups are bonded to the same carbon atom, and this carbon is called an alpha carbon. Amino acids form the backbone of alpha carbon (

) And nitrogen (N) and carbon (C), and hydrogen (H), oxygen (O) or other side chains. Therefore, the group forming unit 120 is an amino acid, that is, alpha carbon (

) And nitrogen (N) and carbon (C), and protein is decomposed by residues.

After the residue decomposition is complete, the group forming unit 120 calculates a distance value between a plurality of atoms contained in the decomposed residue, and uses the calculated distance value to determine the atoms contained within a certain distance based on the center point of the residue. They are grouped (S330).

Hereinafter, a method of forming a group for a residue will be described in more detail using FIG. 5.

5 is a flowchart schematically illustrating step S330 shown in FIG. 3.

As shown in FIG. 5, first, the group forming unit 120 calculates a distance value between atoms included in the decomposed residue (S331). That is, the group forming unit 120 calculates a distance value between atoms using the original coordinates included in the received protein structure data.

와 다른 원자간의 거리를 산출하고, 글라이신이 아닌 경우에는

와 다른 원자간의 거리를 산출한다. In other words, the group forming unit 120 determines whether or not the residue is glycine (GLY). Therefore, when the group forming unit 120 is glycine

Calculate the distance between the and other atoms, and if it is not glycine,

And calculate the distance between the other atoms.

In addition, the group forming unit 120 calculates the distance between atoms using Equation 1 below.

또는

원자의 좌표이고, {(x',y',z'), (x",y",z")...}는 주변 원자의 좌표이다. Where (x,y,z) is

or

The coordinates of the atom, {(x',y',z'), (x",y",z")...} are the coordinates of the surrounding atoms.

Then, the group forming unit 120 sets a cutoff value using the calculated distance value (S332). The cutoff value is a value for a radius applied when grouping residues, and the group forming unit 120 limits the radius required for grouping residues to 10 Å. As described above, the reason for limiting the distance to the radius from the center point to 10 Å is that the average value of the distances of the atoms calculated previously was calculated as 3.63 Å, and the maximum value was calculated as 6.10 Å. As described above, by setting the cutoff value to 10 Å, the group forming unit 120 not only can group all atoms included in the decomposed residue, but also obtain contact information between the corresponding residue and the surrounding residues.

When the setting of the cutoff value is completed as in step S332, the group forming unit 120 acquires information on the atom centered in the residue in order to group all atoms located within a radius of 10 Å (S333).

를 중심점으로 설정하고, 그 외의 잔기일 경우에는 원소 중에서

를 중심점으로 설정한다. That is, the group forming unit 120 sets an atom that is a center in the residue as a center point. Here, when the residue is glycine (GLY), the group forming unit 120 is

Is set as the center point, and in the case of other residues, among the elements

Is set as the center point.

Then, the group forming unit 120 groups all the atoms located within a radius of 10 Å from the obtained central point (S334). At this time, the generated group includes atoms of the corresponding residue located at the center point and other residues located within the set radius.

, N, C 원자를 3차원의 공간 좌표에 표시한다(S340). After the grouping for each decomposed residue is completed as in step S334, the spatial coordinate display unit 130 is included in the grouped residue and corresponds to the backbone of the protein.

, N, C atoms are displayed in three-dimensional spatial coordinates (S340).

Hereinafter, step S340 will be described in more detail with reference to FIGS. 6 to 9.

6 is a flowchart schematically illustrating step S340 illustrated in FIG. 3.

, N, C원자에 대한 정보를 획득한다(S341). 부연하면, 원자 정보 획득모듈(131)은 단백질 백본(backbone)에 위치하며 모든 잔기가 동일하게 가지고 있는

, N, C의 원자에 대한 정보를 획득한다. 여기서,

, N, C의 원자에 대한 정보는 원자 좌표 및 원자간의 거리에 정보를 포함한다. As shown in Fig. 6, the spatial coordinate display unit 130 has the same

, Acquire information on the N, C atoms (S341). In other words, the atomic information acquisition module 131 is located in the protein backbone, and all residues have the same

, N, C to obtain information on the atoms. here,

The information on the atoms of, N, and C includes information on atomic coordinates and distances between atoms.

, N, C원자를 3차원 공간좌표의 XY축의 평면과 평행이 되도록 위치시킨다(S342). 이를 다시 설명하면, 공간좌표 표준화 모듈(132)은

, N, C원자 중에서

를 3차원 공간좌표의 원점과 동일한 위치선상에 위치시킨다. 그 후, 공간좌표 표준화 모듈(132)은

, N, C원자를 3차원 공간좌표의 XY축의 평면과 평행하도록 위치시킨다. Then, the spatial coordinate standardization module 132

, N, C atoms are positioned to be parallel to the plane of the XY axis of the three-dimensional spatial coordinates (S342). To explain this again, the spatial coordinate standardization module 132

, In N, C atoms

Is located on the same position line as the origin of the three-dimensional spatial coordinates. After that, the spatial coordinate standardization module 132

, N, C atoms are positioned parallel to the plane of the XY axis of the 3D spatial coordinates.

, N, C원자와 XY축의 평면이 평행한 상태에서, 공간좌표 표준화 모듈(132)은

원자를 XY축의 원점에 위치시킨다(S343).like this

, In the state that the planes of the N, C atoms and the XY axis are parallel, the spatial coordinate standardization module 132

The atom is placed at the origin of the XY axis (S343).

을 원점에 위치시킨 상태에서 N을 XY축의 평면에 사영시키고, Z축을 중심으로 회전시켜 N을 YZ축의 평면에 위치시킨다(S344). And, the spatial coordinate standardization module 132

N is projected on the plane of the XY axis while being positioned at the origin, and rotated around the Z axis to position N on the plane of the YZ axis (S344).

Hereinafter, step S344 will be described in more detail with reference to FIG. 7.

FIG. 7 is an exemplary diagram schematically showing a method of positioning N on the plane of the YZ axis in step S344 shown in FIG. 6.

벡터와 Y축의 사이에 형성된 사잇각을 추출한다.As shown in FIG. 7, the spatial coordinate standardization module 132 projects N on the plane of the XY axis, and then is projected with respect to the coordinates of N located on the plane of the XY axis.

The intervening angle formed between the vector and the Y axis is extracted.

벡터와 Y축의 사이에 형성된 사잇각을 산출한다. At this time, the spatial coordinate standardization module 132 uses the following Equation 2

The angle formed between the vector and the Y axis is calculated.

는 양의 Y축 벡터값으로서 (0, 1, 0)의 좌표값으로 나타내고,

는 N을 XY평면에 사영 시켰을 때의 벡터값으로 (

,

, 0)의 좌표값으로 나타낸다. here,

Is a positive Y-axis vector value, expressed as a coordinate value of (0, 1, 0),

Is the vector value when N is projected on the XY plane (

,

, 0).

의 값은

이 되고, |

||

| 는 1 ×

의 값을 통해 산출된다. therefore,

Is the value of

Become, |

||

| Is 1 ×

It is calculated through the value of

Then, the spatial coordinate standardization module 132 rotates the Z-axis by an angle so that N contacts the plane of the YZ-axis.

와 동일 선상에 위치하도록 이동시켜 정규화한다(S345). Next, the spatial coordinate standardization module 132 places N located in the plane of the YZ axis into the plane of the XY axis.

It is normalized by moving it to be located on the same line as (S345).

Hereinafter, step S345 will be described in more detail with reference to FIG. 8.

FIG. 8 is an exemplary diagram schematically showing a method of normalizing by placing N on a plane of the XY axis in step S345 shown in FIG. 6.

벡터와 Y축의 사이에 형성된 사잇각을 추출한다. As shown in Figure 8, the spatial coordinate standardization module 132 for coordinates of N located in the plane of the YZ axis

The intervening angle formed between the vector and the Y axis is extracted.

벡터와 Y축의 사이에 형성된 사잇각을 산출한다. At this time, the spatial coordinate standardization module 132 uses Equation 3 below to

The angle formed between the vector and the Y axis is calculated.

는 양의 Y축 벡터값으로서 (0, 1, 0)의 좌표값으로 나타내고,

는 N좌표의 벡터값으로 (0,

,

)의 좌표값으로 나타낸다. here,

Is a positive Y-axis vector value, expressed as a coordinate value of (0, 1, 0),

Is the vector value of N coordinates (0,

,

).

의 값은

이 되고, |

||

| 는 1 ×

의 값을 통해 산출된다. therefore,

Is the value of

Become, |

||

| Is 1 ×

It is calculated through the value of

Then, the spatial coordinate standardization module 132 rotates the X-axis by an angle between the X-axis so that N touches the plane of the XY-axis.

와 N를 정규화 한 다음, 공간좌표 표준화 모듈(132)은 C원자를 XZ축의 평면에 사영시킨 후, 좌표변환 및 회전처리를 이용하여 C원자를 정규화시킨다(S346). As above,

After normalizing and N, the spatial coordinate standardization module 132 projects the C atom on the plane of the XZ axis, and then normalizes the C atom using coordinate transformation and rotation processing (S346).

Hereinafter, step S346 will be described in more detail with reference to FIG. 9.

9 is an exemplary view schematically showing a method of normalizing by placing a C atom on a plane of the XY axis in step S346 shown in FIG. 6.

벡터와 X축의 사이에 형성된 사잇각을 추출한다. As shown in FIG. 9, in a state where the C atom is located parallel to the plane of the XY axis, the spatial coordinate normalization module 132 projects the C atom on the plane of the XZ axis. The spatial coordinate standardization module 132 uses the coordinates of C atoms projected on the plane of the XZ axis.

The intervening angle formed between the vector and the X axis is extracted.

벡터와 X축의 사이에 형성된 사잇각을 산출한다. At this time, the spatial coordinate standardization module 132 uses Equation 4 below.

The angle formed between the vector and the X axis is calculated.

는 양의 x축 벡터값으로서 (1, 0, 0)의 좌표값으로 나타내고,

는 C좌표를 XZ평면에 사영시켰을 때의 벡터값으로 (

, 0,

)의 좌표값으로 나타낸다. here,

Is a positive x-axis vector value, expressed as a coordinate value of (1, 0, 0),

Is the vector value when the C coordinate is projected on the XZ plane (

, 0,

).

의 값은

이 되고, |

||

| 의 값은 1 ×

을 통해 산출된다. therefore,

Is the value of

Become, |

||

| The value of is 1 ×

It is calculated through

와 N와 동일한 위치 선상에 위치하되, C의 좌표는

와 N의 좌표보다 큰 위치값을 가진다. Then, the spatial coordinate standardization module 132 rotates the Y axis by an angle so that the coordinates of C reach the plane of the XY axis. Then, the C atom

It is located on the same position line as and N, but the coordinates of C are

It has a position value greater than the coordinates of and N.

, N, C원자를 XY축의 평면상에 정규화 시킨 다음, 3차원 이미지 변환부(140)는

, N, C원자의 주변에 위치하며 그룹형성부(120)을 통해 그룹화되었던 모든 원자들을 3차원 공간좌표상에 표시하여 이미지화시킨다(S350).Like step S340,

, N, C atoms are normalized on the plane of the XY axis, and then the 3D image conversion unit 140

, N and C atoms are located around the grouping unit 120 to display all the atoms grouped through the three-dimensional spatial coordinates to image (S350).

, N, C의 좌표를 잔기의

가 원점이 되도록 좌표를 이동하여 위치시킨 다음,

를 중심으로

와의 거리가 컷오프 값보다 작은 모든 원자의 좌표를 표시한다. The 3D image conversion unit 140 is normalized on the plane of the XY axis.

, N, C coordinates of the residues

Move and position the coordinates so that is the origin,

Centered on

Displays the coordinates of all atoms whose distance from is less than the cutoff value.

대신에

를 중심으로

와의 거리가 컷오프 값보다 작은 모든 원자의 좌표를 표시한다.On the other hand, when the residue to be imaged is glycine,

Instead of

Centered on

Displays the coordinates of all atoms whose distance from is less than the cutoff value.

FIG. 10 is an exemplary view showing a state in which all elements grouped in step S350 shown in FIG. 3 are displayed in a three-dimensional coordinate space.

또는

를 중심으로

, N, C의 좌표를 위치시키고, 그룹화된 모든 원자들을

, N, C의 주변에 위치하며 3차원 이미지를 생성한다. As shown in FIG. 10, the 3D image conversion unit 140

or

Centered on

Position the coordinates of, N, C, and remove all grouped atoms

, N, and C are located around and create a three-dimensional image.

As described above, according to an embodiment of the present invention, a new possibility of artificial intelligence fusion is possible because it can be used as data for learning data analysis and artificial intelligence models by creating a three-dimensional image representing the amino acid residues of proteins and their surroundings. It has an effect that can be provided as a raw material that will open up.

In addition, according to an embodiment of the present invention, since the normalization process to the same position line is included when performing 3D image generation, it is possible to effectively identify the kind of residue and contact with other residues, and hydrogen removal and channel increase. It is possible to achieve an effect that can be expanded into a desired shape through the like.

The present invention has been described with reference to the embodiments shown in the drawings, but these are only exemplary, and those of ordinary skill in the art will understand that various modifications and equivalent other embodiments are possible therefrom. will be. Therefore, the true technical protection scope of the present invention should be determined by the technical idea of the following claims.

100: 3D image generating device
110: protein data input unit
120: group formation unit
130: spatial coordinate display unit
131: atomic information acquisition module
132: spatial coordinate standardization module
140: 3D image conversion unit

Claims (16)

In an apparatus for generating a three-dimensional image of an environment around an amino acid residue of a protein,
A protein data input unit that receives structural data for a protein,
A group forming unit that calculates the distance between atoms included in each residue constituting the protein using atomic coordinates included in the input structural data of the protein, and forms a group for the residue according to the calculated distance value,
Contained within the group formed above, which is the basic constitution of each residue

, A spatial coordinate display unit that displays N, C atoms in three-dimensional spatial coordinates, and
A 3D image conversion unit displaying all atoms forming the group in the 3D space coordinates,
The group forming unit,
The received protein structure data is used to decompose by residue, calculate the distance between all atoms included in the decomposed residue, and then within a radius with a preset cutoff value from the central atom in the residue. Acquires and groups information about all atoms located,
The central atom is set as the central point, and when the residue is glycine (GLY), among the elements of the residue

Is set as the center point, and in the case of other residues, among the elements

A 3D image generating device that sets as the center point. delete delete The method of claim 1,
The spatial coordinate display unit,
It is located in the protein backbone and all residues have the same

, Atomic information acquisition module that acquires information on the atoms of N, C, and
Obtained from the backbone

, N, C is positioned so that the plane formed by the atoms is parallel to the plane of the XY axis of the three-dimensional spatial coordinates, and is located parallel to the XY axis.

, Among the atoms of N, C

To the origin, and then

A three-dimensional image generating apparatus including a spatial coordinate standardization module that normalizes N and C using coordinate transformation and rotation processing around. The method of claim 4,
The spatial coordinate standardization module,
Among the above three atoms

Move the coordinates so that the coordinates of are located at the origin of the XY axis,
remind

Position N at the origin, project the coordinates of N onto the plane of the XY axis, and then project the coordinates of N at the plane of the XY axis.

By using the angle formed between the vector and the Y axis, the Z axis is rotated so that the coordinates of N reach the plane of the YZ axis,
For the coordinates of the rotated N

Rotate the X axis so that the coordinates of N touch the plane of the XY axis using the angle formed between the vector and the Y axis, and
Projecting the coordinates of C on the plane of the XZ axis,

By rotating the Y-axis so that the coordinates of C touch the plane of the XY-axis by using the angle formed between the vector and the X-axis, the above

, N, C atoms are located in parallel on the plane of the XY axis 3D image generating device. The method of claim 4,
The spatial coordinate standardization module,
remind

With the coordinates of

The vector is parallel to the y-axis, and the coordinates of C are

A 3D image generating apparatus having a position value greater than the coordinates of and N. The method of claim 1,
The 3D image conversion unit,
Normalized on the plane of the XY axis

, N, C coordinates of the residues

Move to the coordinate where is the origin and place it, then

Centered on

A three-dimensional image generating device that displays the coordinates of all atoms whose distance is less than the cutoff value. The method of claim 1,
The 3D image conversion unit,
When the grouped residue is glycine (GLY), normalized on the plane of the XY axis

, N, C of the coordinates

Centered on

A three-dimensional image generating device that displays the coordinates of all atoms whose distance is less than the cutoff value. In a method for generating a three-dimensional image of an environment around an amino acid residue of a protein using a three-dimensional image generating device,
Receiving structural data for the protein,
Calculating the distance between atoms included in each residue constituting the protein using atomic coordinates included in the input structural data for the protein, and forming a group for the residue according to the calculated distance value,
Contained within the group formed above, which is the basic constitution of each residue

, Normalizing atoms of N, C into three-dimensional spatial coordinates, and
Including the step of displaying and imaging all the atoms forming the group in the three-dimensional space coordinates,
The step of forming a group for the moiety,
Decomposing the protein for each residue using the received protein data, and calculating a distance value between atoms included in the decomposed residue,
Setting a cutoff value using the calculated distance value,
Obtaining a central atom from among a plurality of atoms contained in the residue, and
By comparing the calculated distance between the atoms and a cutoff value, all atoms located within a radius having a cutoff value set from the center atom are grouped, and the atoms in the formed group are grouped. Including obtaining information,
When the residue is glycine (GLY), the central atom is among the elements of the residue.

Is set to, and in the case of other residues, among the elements

The 3D image generation method is set to. delete delete The method of claim 9,
The step of normalizing to the three-dimensional spatial coordinates,
It is located in the protein backbone and all residues have the same

, Obtaining information on the atoms of N, C,
Obtained above

, Positioning the plane formed by the atoms of N, C so that it is parallel to the plane of the XY axis of the three-dimensional spatial coordinates, and
Located parallel to the XY axis

, Among the atoms of N, C

To the origin, and then

3D image generation method comprising the step of normalizing the spatial coordinates using the coordinate transformation and rotation processing N and C centered on. The method of claim 12,
Normalizing the spatial coordinates,
Among the above three atoms

Moving the coordinates so that the coordinates of are located at the origin of the XY axis,
remind

Position N at the origin, project the coordinates of N onto the plane of the XY axis, and then project the coordinates of N at the plane of the XY axis.

Rotating the Z-axis so that the coordinates of N touch the plane of the YZ-axis by using the angle formed between the vector and the Y-axis,
For the coordinates of the rotated N

Rotating the X-axis so that the coordinates of N touch the plane of the XY-axis by using the angle formed between the vector and the Y-axis, and
Projecting the coordinates of C on the plane of the XZ axis,

3D image generation method comprising the step of rotating the Y axis so that the coordinates of C contact the plane of the XY axis by using the intervening angle formed between the vector and the X axis. The method of claim 12,
Normalizing the spatial coordinates,
remind

With the coordinates of

The vector is parallel to the y-axis, and the coordinates of C are

A 3D image generation method that is located larger than the coordinates of and N. The method of claim 9,
The imaging step,
Normalized on the plane of the XY axis

, N, C coordinates of the residues

Move to the coordinate where is the origin and place it, then

Centered on

A three-dimensional image generation method that displays the coordinates of all atoms whose distance from is less than the cutoff value. The method of claim 9,
The imaging step,
When the grouped residue is glycine (GLY),
Normalized on the plane of the XY axis

, N, C of the coordinates

Centered on

A three-dimensional image generation method that displays the coordinates of all atoms whose distance from is less than the cutoff value.

Images