JP5734586B2 - Sugar chain structure recognition analysis method, sugar chain structure recognition analyzer and program - Google Patents

Description

  The present invention relates to an analysis method, an analysis apparatus, and a program for recognizing a sugar chain structure, and specifically, an analysis for recognizing a chemical structure of a sugar chain comprising a monosaccharide of a chair type conformation. The present invention relates to a method, an analysis apparatus, and a program.

  The sugar chain is positioned as the third life chain following the nucleic acid that carries genetic information and the protein that constitutes the biofunctional molecule, and its important characteristic is its structural diversity. Nucleic acids are composed of 4 types of bases, proteins are composed of 20 types of amino acids and are arranged in a row, whereas sugar chains are chained substances composed of monosaccharides such as glucose and galactose. Since a plurality of hydroxyl groups possessed by can be used for bonding, a complicated structure can be created as shown in FIG.

  When describing the structure of a glycan two-dimensionally, it is customary to identify and express the glycan by combining the monosaccharides that are identified by the monosaccharide unit that is the component, and combining the recognized saccharides. Yes. However, as shown in FIG. 2, as a method of drawing a cyclic form of a monosaccharide, Fischer projection, Haworth projection, Mills display, conformation-considered display format (hereinafter referred to as conformation display), Glc, and the like are simplified. There are multiple notation methods such as string abbreviations, which are not uniform. Further, for example, when β-D-glucose is drawn by conformation display, the difference in the observation direction and the conformation in the drawing of the three-dimensional structure, as shown in FIG. Drawn on the street.

On the other hand, in order to specify the structure of a monosaccharide, it is necessary to determine the bonding direction of the hydroxyl group bonded to the 6-membered ring carbon in the three-dimensional structure and to distinguish between the α / β isomer and the L isomer / D isomer. is there. Furthermore, for chair-type conformational sugars, it is necessary to distinguish between two isomers, ¹ C ₄ and ⁴ C ₁ . Therefore, in order to identify the structure of a monosaccharide that constitutes a sugar chain drawn by a certain notation method, a process for determining the direction of the hydroxyl group and identifying the type of monosaccharide that is the parent of the partial structure in the sugar chain, And the process which recognizes that each chemical structural formula shown by FIG. 3 is the same compound is needed. In addition, for sugar chains, it is necessary to determine in which direction the monosaccharides adjacent to each other are bound using which hydroxyl group.

  The database on chemical information is not only an indispensable tool in modern chemical and drug discovery research, but also an indispensable tool for patent information and reagent management. Known application programs that allow a computer to handle chemical information as data include ISIS Draw, ChemDraw (registered trademark), and ACD / ChemSketch. In addition, as a function for supporting the input of chemical information, a system that enables input of a corresponding chemical structural formula by specifying a chemical abbreviation or a template has been proposed.

JP-T-2003-531419 Japanese translation of PCT publication No. 2003-502773

M. Arita, T. Tokimatsu, ‘‘ Detection of monosaccharide types from coordinates ’’, Proceedings of the 18th International Conference on Genome Informatics (Genome Informatics Series Vol. 19) pp3-14, 2007.

  As described above, the systematization of chemical information is progressing, and it is possible to provide useful information that supports research and development. Also, the cost of inputting chemical structural formulas when using the system has been reduced. However, it is not sufficient in confirming whether the inputted chemical structural formula is the intended chemical structural formula. For example, when a data creator inputs a chemical structural formula, a similar chemical structural formula that has already been input may be modified to create a new structural formula. At this time, there is a possibility that a chemical structural formula different from the intended structure may be created due to omission of correction or improper modification. However, as described above, the substance having a complicated chemical structure is confirmed accurately. It is difficult.

  If a mistake is made at the stage of entering a chemical structure, it will not be used in subsequent data retrieval, providing incorrect information, or using a wrong chemical structure will lead to a second erroneous entry. It develops into a problem that suffers.

  The present invention has been made in view of such problems, and the object of the present invention is to use simplified symbols and abbreviations in order to determine whether or not an inputted chemical structural formula is accurate. An object of the present invention is to provide an analysis method, an analysis apparatus, and a program that support a user's structural recognition by displaying a chemical structural formula.

The inventors have, in the structure recognition of the monosaccharide of the chair conformation, by using a given Calculated for constituting atom, which has heretofore been impossible alpha / beta isomer, and _¹ C ^_4/4 C ¹ isomer I found that I can distinguish the body. Based on this knowledge, an analysis method, an analysis apparatus, and a program for recognizing a chemical structure of a sugar chain having a chair type conformation monosaccharide as a constituent element have been completed.

  The invention according to claim 1 is an analysis method for recognizing a chemical structure of a sugar chain comprising a monosaccharide of a chair type conformation as a constituent element, the step of receiving chemical structural formula data to be analyzed; Based on the step of extracting the partial structure of the monosaccharide from the received chemical structural formula data to be analyzed, the step of acquiring the positional information of the constituent atoms for the extracted partial structure of the monosaccharide, and the acquired positional information Calculating an outer product of a mode vector having an inner angle of a ring of a monosaccharide and an angle forming the inner angle, and an outer product of the mode vector and the inner angle based on the outer product of the calculated mode vector and the calculated inner angle And a mode table for associating the mode with each other, determining a mode of the rotational structure of the monosaccharide, and based on the acquired position information, orientation determination target atoms, Calculates the outer product of the orientation vectors having the angle formed by the first ring member atom bonded to the orientation determination target atom and the second ring member atom adjacent to the first ring member atom. Determining the orientation of the orientation determination target atom based on the outer product of the orientation vector, the inner angle, the acquired position information, and the determined mode, the determined rotational structure, and the determined orientation And a step of converting the chemical structure of the monosaccharide to be analyzed into a corresponding abbreviation using an abbreviation table that associates the monosaccharide abbreviation with the chemical structure, and outputting the converted abbreviation. It is characterized by including.

  Invention of Claim 2 is the analysis method for recognizing the chemical structure of the sugar chain which uses the monosaccharide of the chair type | mold conformation of Claim 1 as a component, Comprising: The coupling | bonding information between ring member atoms The step of determining the mode determines the mode based on the acquired combined information, and the step of determining the direction determines the direction based on the acquired combined information. It is characterized by.

  The invention according to claim 3 is an analysis apparatus for recognizing a chemical structure of a sugar chain comprising a monosaccharide of a chair type conformation as a constituent element, and receives a chemical structural formula data to be analyzed. A data reception unit; a partial structure search unit that extracts a partial structure of a monosaccharide from the received chemical structural formula data to be analyzed; and position information acquisition that acquires positional information of constituent atoms for the extracted partial structure of the monosaccharide A first ring structure that binds to the orientation determination target atom and the orientation determination target atom, the inner product of the ring of the monosaccharide based on the acquired position information, the outer product of the mode vectors as the angle forming the internal angle A calculation unit for calculating an outer product of orientation vectors having an angle formed by an atom and a second ring-constituting atom adjacent to the first ring-constituting atom; an outer product of the mode vector and the inner angle; Associate a mode A storage unit that manages a mode table, an abbrev table for associating an abbreviation of a monosaccharide with a chemical structure, a monosaccharide using the mode table based on the outer product of the calculated mode vector and the calculated inner angle A mode determination unit that determines the mode of the rotational structure of the direction determination unit, and a direction determination unit that determines the direction of the orientation determination target atom based on the outer product of the direction vectors, the inner angle, the acquired position information, and the determined mode And based on the determined rotational structure and the determined orientation, a data conversion unit that converts the chemical structure of the monosaccharide to be analyzed into a corresponding abbreviation using the abbreviation table, and the converted abbreviation And an output unit for outputting.

  Invention of Claim 4 is an analyzer for recognizing the chemical structure of the sugar chain which uses the monosaccharide of the chair type conformation of Claim 3 as a constituent element, Comprising: Bonding information between ring constituent atoms The mode determination unit determines a mode based on the acquired combination information, and the direction determination unit determines a direction based on the acquired combination information. Features.

Invention of Claim 5 is a program, Comprising: It makes a computer perform the analysis method for sugar chain structure recognition of Claim 1 or 2.

  According to the present invention, a data creator of a chemical structural formula can visually and intuitively determine whether the created chemical structural formula matches the target chemical structural formula. Furthermore, when the created chemical structural formula does not match the intended chemical structural formula, it is possible to easily correct the unintended chemical structural formula to the intended chemical structural formula.

It is a figure which shows the branched structure of sugar chain. It is a figure which shows the notation method which draws the cyclic | annular form of a monosaccharide. It is a figure which shows the rotation structure of (beta) -D-glucose. It is a block diagram which shows the chemical structure recognition assistance system concerning one Embodiment of this invention. It is a module block diagram of the chemical structural formula analysis server concerning one Embodiment of this invention. It is a flowchart which shows the whole process for recognizing the chemical structure of the sugar chain which uses the monosaccharide concerning one Embodiment of this invention as a component. It is a figure which shows the chemical structural formula of the analysis object concerning one Embodiment of this invention. It is a figure which shows the numbered monosaccharide concerning one Embodiment of this invention. It is a flowchart which shows the process which determines the rotation structure of the monosaccharide represented by the conformation display concerning one Embodiment of this invention. It is a flowchart which shows the process which determines the direction of the hydroxyl group of the monosaccharide represented by the conformation display concerning one Embodiment of this invention. It is a figure which shows the information allocated to a 6-membered ring member atom in the process which determines the direction of the hydroxyl group of the monosaccharide concerning one Embodiment of this invention. It is a flowchart which shows the process which determines the direction of the hydroxyl group of the monosaccharide represented by the conformation display concerning one Embodiment of this invention. It is a flowchart which shows the process which determines the direction of the hydroxyl group of the monosaccharide represented by the conformation display concerning one Embodiment of this invention. It is a figure which shows the area | region information used for determination in the process which determines the direction of the hydroxyl group of the monosaccharide concerning one Embodiment of this invention. It is a figure which shows an example of the information stored in mode DB concerning one Embodiment of this invention. It is a figure which shows an example of the information stored in the abbreviation DB concerning one Embodiment of this invention. It is a figure which shows an example of the result screen which analyzed the chemical structural formula concerning one Embodiment of this invention. It is a figure which shows the example of a conversion of the result screen which analyzed the chemical structural formula concerning one Embodiment of this invention. It is a figure which shows the example of a conversion of the result screen which analyzed the chemical structural formula concerning one Embodiment of this invention. It is a figure which shows the example of a conversion of the result screen which analyzed the chemical structural formula concerning one Embodiment of this invention.

  FIG. 4 is a block diagram showing a chemical structure recognition support system according to an embodiment of the present invention. A client computer 401 used by a data creator who inputs a chemical structural formula, which implements a chemical structure recognition support system, and a chemical structural formula analysis server 403 are configured to communicate via a network 402. The client computer 401 includes display means such as a liquid crystal display and input means such as a mouse and a keyboard. The network 402 of the present embodiment can use an Internet communication network known in this technical field, but is not limited to this, and a dedicated or general-purpose network can be used.

  FIG. 5 is a module configuration diagram of the chemical structural formula analysis server according to the embodiment of the present invention. The chemical structural formula analysis server 403 includes a chemical structural formula data receiving unit 501 that receives chemical structural formula data to be analyzed from the client computer 401, and a partial structural search unit 502 that extracts a specific partial structure from the chemical structural formula data to be analyzed. A position information acquisition unit 503 that acquires position information of constituent atoms, a calculation unit 504 that calculates a specific angle and a cross product based on the acquired position information, and a mode determination unit 505 that determines a mode representing a rotation structure of a monosaccharide , A direction determination unit 506 for determining the direction of the hydroxyl group of a monosaccharide, a data conversion unit 507 for converting a monosaccharide to an abbreviation based on the analysis result, a storage unit 508 for managing related data, and displaying the analysis result on a client computer An analysis result output unit 509 that provides a screen is provided.

  The storage unit 508 manages a mode DB that stores information related to a mode representing the rotational structure of a monosaccharide, and an abbreviation DB that stores information related to an abbreviation of the monosaccharide. Although the module configuration of the present embodiment has been described above, this is merely an example, and each module can be further disassembled for each function, or can be mounted assuming a new module in which the functions of each module are integrated. .

(Whole process for recognizing the chemical structure of a sugar chain consisting of monosaccharides
FIG. 6 is a flowchart showing an overall process for recognizing a chemical structure of a sugar chain having a monosaccharide as a constituent element according to an embodiment of the present invention. In process S601, the chemical structural formula receiving unit 501 receives chemical structural formula data of a sugar chain as shown in FIG. 7, which is an example of the present embodiment as a chemical structure to be analyzed. This chemical structural formula data can be received from the user or from an external system via the client computer 401.

  In process S602, the partial structure search unit 502 extracts a six-membered ring from the received chemical structural formula data. In this embodiment, ten 6-membered rings are extracted. From step S603 onward, iterative processing is performed on all six-membered rings extracted in step S602.

  In step S603, the position information acquisition unit 503 performs numbering on the six-membered ring constituent atoms, and the oxygen atoms (0 atoms) and carbon atoms (C atoms) bonded to the constituent atoms based on the ranking rule. FIG. 8 shows a numbered monosaccharide according to an embodiment of the present invention. Further, the position information acquisition unit 503 acquires the position information of the numbered atoms.

  In process S604, the calculation unit 504 calculates outer products c1k to c5k and o5k of vectors having angles forming the inner angle of the six-membered ring. Specifically, the outer product of C1 → O5 and C1 → C2 (c1k), the outer product of C2 → C1 and C2 → C3 (c2k), the outer product of C3 → C2 and C3 → C4 (c3k), C4 → C3 and C4 → Calculate the outer product of C5 (c4k), the outer product of C5 → C4 and C5 → O5 (c5k), and the outer product of O5 → C5 and O5 → C1 (o5k).

  In step S605, the calculation unit 504 calculates the absolute value of the sum of the SIGN function of the outer product calculated in step S604, which is expressed by the following mathematical formula 1.

  In the process S606, when the calculated absolute value is not 6, it is determined that the monosaccharide to be analyzed is described in the conformation display, and the process proceeds to the process S607. When the calculated absolute value is 6, it is determined that the monosaccharide to be analyzed is described in Mills display, and the process proceeds to step S608. In the present embodiment, since the calculated absolute value is 2, the process proceeds to step S607.

  As will be described later, in processing S607 or S608, analysis processing according to each notation method is performed, and in processing S609, the data conversion unit 507 converts the chemical structural formula based on the analysis result.

  In process S610, it is determined whether or not the analysis has been completed for all the six-membered rings extracted in process S602. If the analysis has not been completed for all the six-membered rings, the process returns to the process S603 and the processes S603 to S610 are repeated.

  If the analysis has been completed for all the six-membered rings, in step S611, the analysis result output unit 509 provides a screen for displaying the analysis results on the client computer, and the processing ends.

(Process to determine the rotation structure of monosaccharides)
FIG. 9 is a flowchart showing a process for determining a rotation structure of a monosaccharide represented by a conformation display according to an embodiment of the present invention. Following the processing S606 in FIG. 6, the rotation structure of the monosaccharide shown in FIG. 8 is determined.

In the process S901, the mode determination unit 505 identifies the reference angle using the mode DB based on the outer product calculated in the process S604 of FIG. As shown in FIG. 15, the mode DB has attributes related to at least the sign of the outer product, the reference angle, the acute angle flag, the ⁴ C ₁ mode, and the ¹ C ₄ mode. The reference angle is one of the inner angles of the six-membered ring, and can be specified by a combination of outer product codes. For example, in this embodiment, the signs of the outer product c1k, outer product c3k, outer product c4k, and outer product o5k are negative, and the signs of the outer product c2k and outer product c5k are positive, so the reference angle is C1. The acute angle flag indicates whether the reference angle is an acute angle.

In process S902, the calculation unit 504 calculates the angle of the reference angle, and the mode determination unit 505 uniquely identifies the record in the mode DB based on whether or not the reference angle is an acute angle. As shown in FIG. 15, the record of the mode DB is uniquely identified by the combination of the sign of the outer product of vectors that form the inner angle of the six-membered ring and the acute angle flag, and the mode is ^one of the ¹ C ₄ modes. And one of ⁴ C ₁ modes. For example, in the present embodiment, since the reference angle C1 determined by the code of the outer product is an acute angle, the mode determination unit 505 identifies the record whose ID is 1, and the mode is ⁴ C ₁ +0 or ¹ C ₄ +180. It is narrowed down to either.

In process S903, the calculation unit 504 calculates the Z-axis rotation angle, and the mode determination unit 505 determines the mode based on the Z-axis rotation angle. The Z-axis rotation angle is an angle rotated in the Z-axis direction from the standard structure (shown in FIG. 3) for the ⁴ C ₁ mode of the record specified in step S902. Specifically, the mode determination unit 505 determines that the mode is the ⁴ C ₁ mode when the Z-axis rotation angle is 90 degrees or less or 270 degrees or more, and otherwise determines that the mode is the ¹ C ₄ mode. Determine and provisionally specify one mode. In the present embodiment, since the rotation from the standard structure with respect to ⁴ C ₁ +0 of the specified record is 0 degree, the mode is provisionally specified as ⁴ C ₁ +0.

Further, in process S904, the mode determination unit 505 determines the final mode in consideration of the wedge, and then rotates the y-axis after rotating in the Z-axis direction so as to become a standard structure among the six-membered ring constituent atoms. It is determined whether or not any of the three bonds connecting the three constituent atoms located above and the constituent atom that is the apex of the acute angle on the lower side is represented by a wedge. In the present embodiment, the three bonds connecting the three constituent atoms (C4 atom, C5 atom, O5 atom) located on the y-axis and the lower sharp vertex (C1 atom) are as follows: Since it is not represented by a wedge, the monosaccharide mode is fixed at ⁴ C ₁ +0, and the process ends.

If it is determined in the process S904 that it is written as a wedge, in the process S905, the mode determination unit 505 exchanges the modes 4 and 1, and ± determined in the process S903. For example, when the corresponding bond of the monosaccharide determined to be ⁴ C ₁ +60 in the process S903 is represented by a wedge, the mode is fixed to ¹ C ₄ -60 by the process S905.

(Process to determine the orientation of the hydroxyl group of a monosaccharide)
Next, processing for determining the orientation of the hydroxyl group of a monosaccharide will be described with reference to FIGS. In process S1001, the direction determination unit 506 determines whether or not an O1 atom to an O4 atom or a C6 atom is bonded to a six-membered ring constituent atom. In the case of bonding, the orientation of the hydroxyl group is determined by the processing after processing S1003. When the orientation of the hydroxyl group is determined in any process, the process returns to process S1002 (not shown).

  When the O1 atom to O4 atom or the C6 atom is not bonded, in step S1002, the direction determination unit 506 determines whether the analysis of all the six-membered ring atoms has been completed. When the analysis of all 6-membered ring atoms has been completed, the process for determining the direction of the hydroxyl group of the monosaccharide is completed. If the analysis has not ended, the process returns to step S1001 again, and the analysis is performed on the unanalyzed six-membered ring constituent atoms.

  In process S1003, as shown in FIG. 11, the calculation unit 504 sets C atoms connected to any one of O1 to O4 atoms or C6 atoms as C_connect, and sets two six-membered ring atoms adjacent to C_connect, respectively. When C_neighbor1 and C_neighbor2 are set, the outer product o_1 of C_connect → C_neighbor1 and C_connect → O (or C6) and the outer product o_2 of C_connect → C_neighbor2 and C_connect → O (or C6) are calculated.

  In step S1004, the direction determination unit 506 determines whether the interior angle ck configured by C_neighbor1-C_connect-C_neighbor2 is less than 90 degrees. When the inner angle ck is less than 90 degrees, the process proceeds to step S1005, and when the inner angle ck is 90 degrees or more, the process continues to FIG. In the present embodiment, in the case of c1k and c4k, it is determined that the internal angle ck is less than 90 degrees, and the process proceeds to step S1005.

  In process S1005, the orientation determination unit 506 determines whether the signs of the outer products o_1 and o_2 calculated in process S1003 are both positive, negative, or other. When the signs of the outer products are both positive, the process proceeds to step S1006, and the orientation determination unit 506 determines the final orientation of the hydroxyl group based on the position of C_connect. When the signs of the outer products are both negative, the process proceeds to step S1007, and the orientation determination unit 506 determines the final orientation of the hydroxyl group based on the position of C_connect.

  Here, the position of C_connect is the 6-membered ring constituent atoms that are the vertices of the two inner angles determined to be less than 90 degrees in process S1004 when rotated in the Z-axis direction so as to have a standard structure. Indicates whether C_connect is right or left on the x-axis relative to the other. In the present embodiment, the C1 atom that is the apex of c1k is right on the x-axis, and the C4 atom that is the apex of c4k is left on the x-axis.

  Regarding the hydroxyl group bonded to the C1 atom, it is determined in process S1005 that both signs of the outer product are positive, and in process S1006 it is determined that C_connect is located on the right, indicating that it is upward. Regarding the hydroxyl group bonded to the C4 atom, it is determined in process S1005 that both signs of the outer product are positive, and in process S1006, it is determined that C_connect is located on the left, and it can be seen that it is downward.

  When the sign of the outer product is other, the direction of the hydroxyl group is determined to be intermediate between upward and downward.

Here, the orientation of the hydroxyl group determined through FIG. 10, FIG. 12, and FIG. 13 is “a monosaccharide in which the mode is a ⁴ C ₁ mode and the bond determined in step S904 is not represented by a wedge” or The results are shown for “a monosaccharide in which the mode is ¹ C ₄ mode and the binding determined in step S904 is represented by a wedge”. When the above-mentioned conditions are not satisfied, the direction of the hydroxyl group is upside down.

  If it is determined in process S1004 of FIG. 10 that the internal angle ck is 90 degrees or more, the process proceeds to FIG. Judge whether. When the inner angle ck is less than 180 degrees, the process proceeds to step S1202, and when the inner angle ck is 180 degrees or more, the process continues to FIG. In the present embodiment, in the case of c3k and o5k, it is determined that the internal angle ck is less than 180 degrees, and the process proceeds to step S1202.

  In process S1202, as shown in FIG. 11, when the six-membered ring atoms located on the opposite side of C_connect is C_diagonal, the calculation unit 504 has a slope of C_connect → C_diagonal among C_connect → C_neighbor1 and C_connect → C_neighbor2 Calculate the outer product of the closest one and C_connect → O (or C6). Here, that the inclination is close means that the difference in inclination with respect to the x-axis is small.

  In process S1203, the direction determination unit 506 determines whether the calculated sign of the outer product is 1, −1, or 0. If Sign is 1, the process proceeds to step S1204, and the orientation determination unit 506 determines the final orientation of the hydroxyl group based on the position of C_connect. When Sign is −1, the process proceeds to step S1205, and the orientation determination unit 506 determines the final orientation of the hydroxyl group based on the position of C_connect.

  Here, the position of C_connect is the six-membered ring constituent atoms that are the vertices of the two inner angles that are determined to be less than 180 degrees in process S1201 when rotated in the Z-axis direction so as to have a standard structure. Indicates whether C_connect is right or left on the x-axis relative to the other. In the present embodiment, the C3 atom that is the apex of c3k is on the left on the x-axis. With respect to the hydroxyl group bonded to the C3 atom, it is determined that Sign is −1 in process S1203, it is determined to be located to the left of C_connect in process S1205, and it can be seen that it is upward.

  When Sign is 0, the direction of the hydroxyl group is determined to be intermediate between upward and downward.

  If it is determined in process S1201 of FIG. 12 that the internal angle ck is 180 degrees or more, the process proceeds to FIG. 13, and in process S1301, the orientation determination unit 506 determines whether the position of C_connect → O (or C6) is region 1 or not. It is determined whether it is area 2 or other. Here, region 1 represents a region outside the six-membered ring, as shown in FIG. As illustrated in FIG. 13, the region 2 represents a region that is symmetric with respect to the region 1 and includes an extension line of the C_neighbor1-C_connect coupling and an extension line of the C_neighbor2-C_connect coupling.

  When the position of C_connect → O (or C6) is the region 1, the process proceeds to step S1302, and the orientation determination unit 506 determines the final hydroxyl orientation based on the location of C_connect. When the position of C_connect → O (or C6) is the region 2, the process proceeds to step S1303, and the orientation determination unit 506 determines the final orientation of the hydroxyl group based on the location of C_connect.

  Here, the position of C_connect is a 6-membered ring configuration that is the apex of the two inner angles that are determined to be 180 degrees or more in step S1201 of FIG. 12 when rotated in the Z-axis direction so as to have a standard structure. Indicates whether C_connect of atoms is up or down on the y-axis relative to the other. In this embodiment, the C2 atom that is the apex of c2k is down on the y-axis, and the C5 atom that is the apex of c5k is up on the y-axis. With respect to the hydroxyl group bonded to the C2 atom, it is determined in step S1301 that the position of C_connect → O is region 1, and in step S1302, it is determined that C_connect is positioned below, indicating that it is downward. For the C6 atom bonded to the C5 atom, the position of C_connect → C6 is determined to be the region 1 in the process S1301, and it is determined that the C_connect is positioned upward in the process S1302, and it can be seen that it is upward.

  If the position of C_connect → O (or C6) is other than that, the direction of the hydroxyl group is determined to be intermediate between upward and downward.

(Process to convert chemical structural formula of monosaccharide to abbreviation)
Through the processes of FIGS. 9, 10, 12, and 13, the mode of monosaccharide and the direction of hydroxyl group can be determined. In order to specify the abbreviation for the chemical structural formula of the monosaccharide, the data conversion unit 507 uses (1) whether or not there is a C0 atom bonded to the C1 atom as information necessary for the conversion, and (2) C6 Whether or not an atom is present, (3) whether or not a substituent is present, the type of the substituent, and the like are acquired from the chemical structural formula data. Unlike the determination of the mode and the direction of the hydroxyl group, such information can be easily determined based on the information of specific constituent atoms constituting the chemical structural formula, and thus will not be described in detail here.

  After acquiring information necessary for the conversion, the data conversion unit 507 generates symbol data indicating the presence / absence of the C0 atom and the C6 atom and the direction of the group bonded to the C2 atom to the C5 atom. In this embodiment, with respect to the C0 atom and the C6 atom, “/” is used when there is no constituent atom, “|” is used when there is a constituent atom, and the group bonded to the C2 to C5 atoms is oriented. “+” Is used when is upward, “−” is downward, and “*” is used when there is no group bonded to the constituent atom. For example, in the case of the monosaccharide shown in FIG. 8, “C0 / C2−C3 + C4−C5 + C6 |” is generated.

  The data conversion unit 507 accesses the abbreviation DB via the storage unit 508, and acquires a monosaccharide abbreviation corresponding to the created symbol data. As shown in FIG. 16, the abbreviation DB has at least attributes relating to symbols corresponding to abbreviations and abbreviations of monosaccharides. If there is no record corresponding to the created symbol data, it indicates that the chemical structure is not recognizable as sugar. Next, the data conversion unit 507 determines α / β based on the direction of the hydroxyl group bonded to the C1 atom, and further specifies a final abbreviation in consideration of a substituent and the like.

(Process to output analysis results)
After the analysis is completed for all monosaccharides, the analysis result output unit 509 transmits the analysis results as shown in FIG. 17 to the client computer 401 for display. In this embodiment, it is assumed that the data creator creates data for the purpose of a sugar chain composed of β-D-GlcNAc. As shown in FIG. 17, the chemical structural formula to be analyzed includes one unintended β-D-GalNAc, β-L-GalNAc, and β-D-All, two β-L-GlcNAc, and It turns out that one thing which cannot be recognized as a monosaccharide is contained. When the data creator gives a conversion instruction using an input means such as a keyboard or mouse, the data conversion unit 508 converts the current display form (abbreviation) to another display form (chemical structural formula, numbering display, etc.) The analysis result output unit 509 can transmit the analysis results as shown in FIGS. 18 to 20 to the client computer 401 for display.

  FIG. 18 is a conversion example of the analysis result shown in FIG. 17 and shows the analysis result in which monosaccharides are expressed in numbering display. FIG. 19 is an example of conversion of the analysis result shown in FIG. 17 and shows the analysis result in which monosaccharides are expressed in conformation. FIG. 20 is a conversion example of the analysis result shown in FIG. 17 and shows the analysis result in which monosaccharides are represented by abbreviations and numbering displays. Note that, as shown in FIGS. 17 and 20, the abbreviations are given colors that are commonly used in this field. A person skilled in the art can grasp the structure of a monosaccharide by the shape of abbreviation (square, circle, etc.) and color (yellow, light blue, etc.). For example, GlcNAc-β is represented by a light blue square, and GalNAc-β is represented by a yellow square. In addition, even a user who is not familiar with this field can grasp the numbering information and conformation of the six-membered ring constituent atoms by converting the analysis result.

  As described above, according to the present invention, the data creator of the chemical structural formula can visually and intuitively determine whether the created chemical structural formula matches the target chemical structural formula. Furthermore, when the created chemical structural formula does not match the intended chemical structural formula, it is possible to easily correct the unintended chemical structural formula to the intended chemical structural formula.

Claims (5)

An analysis method for recognizing the chemical structure of a sugar chain comprising a monosaccharide of a chair type conformation,
Receiving chemical structure data to be analyzed;
Extracting a partial structure of a monosaccharide from the received chemical structural formula data to be analyzed;
Obtaining positional information of constituent atoms for the extracted partial structure of the monosaccharide;
Based on the acquired positional information, calculating an inner product of a ring of monosaccharides, and an outer product of mode vectors as angles forming the inner angle;
Determining a mode of the rotational structure of the monosaccharide using a mode table that associates the outer product of the mode vector and the inner angle with the mode based on the outer product of the calculated mode vector and the calculated inner angle;
Based on the acquired position information, it is composed of an orientation determination target atom, a first ring constituent atom bonded to the orientation determination target atom, and a second ring constituent atom adjacent to the first ring constituent atom. Calculating an outer product of orientation vectors whose angles form an angle to be formed;
Determining the orientation of the orientation determination target atom based on the outer product of the orientation vector, the interior angle, the acquired position information, and the determined mode;
Converting the chemical structure of the monosaccharide to be analyzed into a corresponding abbreviation using an abbreviation table that associates the abbreviation of the monosaccharide with the chemical structure based on the determined rotational structure and the determined orientation; and ,
And a step of outputting the converted abbreviation. Further comprising obtaining bond information between ring members,
The step of determining the mode determines a mode based on the acquired combination information,
The sugar chain structure recognition analysis method according to claim 1, wherein in the step of determining the direction, the direction is determined based on the acquired binding information. An analyzer for recognizing the chemical structure of a sugar chain comprising a monosaccharide of a chair type conformation,
A chemical structure data receiver for receiving chemical structure data to be analyzed;
A partial structure search unit for extracting a partial structure of a monosaccharide from the received chemical structural formula data to be analyzed;
A positional information acquisition unit that acquires positional information of constituent atoms for the extracted partial structure of the monosaccharide;
Based on the acquired position information, the inner angle of the ring of the monosaccharide, the outer product of the mode vector as the angle forming the inner angle, the orientation determination target atom, and the first ring constituent atom bonded to the orientation determination target atom, A calculation unit for calculating an outer product of orientation vectors having an angle formed by a second ring-constituting atom adjacent to the first ring-constituting atom;
A storage unit that manages a mode table that associates the outer product of the mode vector and the inner angle with the mode, and an abbreviation table that associates the abbreviation of the monosaccharide with the chemical structure;
Based on the outer product of the calculated mode vector and the calculated inner angle, a mode determination unit that determines the mode of the rotation structure of the monosaccharide using the mode table;
An orientation determination unit that determines the orientation of the orientation determination target atom based on the outer product of the orientation vector, the interior angle, the acquired position information, and the determined mode;
Based on the determined rotational structure and the determined orientation, a data conversion unit that converts the chemical structure of the monosaccharide to be analyzed into the corresponding abbreviation using the abbreviation table;
An analyzer for recognizing a sugar chain structure, comprising: an output unit that outputs the converted abbreviation. It further includes a bond information acquisition unit that acquires bond information between ring atoms,
The mode determination unit determines a mode based on the acquired combination information,
The sugar chain structure recognition analysis apparatus according to claim 3, wherein the direction determination unit determines a direction based on the acquired binding information. A program that causes a computer to execute the analysis method for sugar chain structure recognition according to claim 1 or 2.