JP2679765B2 - Protein secondary structure simulation system - Google Patents

Description

DETAILED DESCRIPTION OF THE INVENTION [Outline] The present invention relates to a protein secondary structure simulation system, which corresponds to a protein to be predicted from among a plurality of types of prediction simulation programs for predicting secondary structure from primary structure of protein. A protein secondary structure simulation system for selecting a prediction simulation program, wherein secondary structure measurement values corresponding to the primary structure of a predetermined protein and secondary structure predictions of the plurality of types of prediction simulation programs respectively predicted for the primary structure The determination result of the prediction accuracy obtained by comparing with the value is stored in association with the primary structure to store a determination result database, and a primary structure similar to the primary structure of the prediction target protein given from the determination result database. Search the structure and the corresponding judgment result data And a search unit for displaying.

[Industrial applications]

The present invention relates to improvement of a protein secondary structure simulation system.

Prediction from the secondary structure of protein secondary structure using a computer has been attempted by many people, and several kinds of methods have been established.

However, although each method shows a good agreement with the measured value for a group with a protein, the result that the probability of a match is significantly reduced when the group changes is obtained. Therefore, in order to improve the prediction accuracy, It is necessary to select an optimal prediction method (prediction simulation program) for the group to be predicted.

However, since a prediction simulation program is conventionally selected by the user's judgment, there is a problem that an accurate prediction method cannot be efficiently selected, and a prediction simulation system that solves this problem is required.

[Problems to be solved by conventional technology and invention]

 FIG. 6 is an explanatory diagram of a protein structural analysis procedure.

As is well known, proteins are made up of 20 or more kinds of amino acid residues linked in a chain.

These amine acid residues are linked by a peptide bond, and the bond representation by the sequence of their designation symbols, for example, the designation symbols such as alanine = A and glutamic acid = E, is called the primary structure of the protein.

Generally, it is said that the properties of a protein are determined by its shape (tertiary structure), and its shape is uniquely determined by its primary structure.

For this reason, analyzers that seek the primary structure of proteins are now undergoing remarkable development, and the primary structures of many proteins are required.

However, conversely, the theory for determining the shape (tertiary structure) of a protein from its primary structure has not been established at present, and various methods have been tried.

Most of these methods do not directly determine the tertiary structure from the primary structure of the protein, but rather the core structure (secondary structure) and then the tertiary structure. Many methods have been developed for seeking.

The secondary structure shows a fixed structure such as a helix or a sheet as shown in Fig. 6, and does not depend on a unique amino acid sequence but shows a uniform shape by a plurality of amino acid sequences. Since the structure of is relatively stable, it is difficult for the structure to change even during the folding process.

Therefore, the method of obtaining the entire tertiary structure after obtaining the secondary structure which is the core of the tertiary structure from the primary structure is a very effective means.

As described above, several kinds of methods for predicting secondary structure rather than primary structure of protein have been developed, and with the help of a computer, a prediction simulation program for predicting and displaying the prediction result has been developed. , Because the groups with good prediction accuracy differ for each method,
In order to improve the prediction accuracy, it is necessary to select the optimum prediction simulation program based on the primary structure of the prediction target.

However, in the past, since the selection was made by the user's judgment, there was a problem that an accurate method could not be selected efficiently.

In view of the above problems, it is an object of the present invention to provide a protein secondary structure simulation system that can provide prediction accuracy information of various prediction simulation programs to make efficient predictions.

[Means for solving the problem]

In order to achieve the above-mentioned object, the protein secondary structure simulation system of the present invention is, as shown in the principle diagram of FIG. 1 of the present invention, a plurality of types of prediction simulation programs for predicting secondary structure from primary structure of protein (11 A) a secondary structure simulation system for selecting a prediction simulation program adapted to a protein to be predicted from among A) and B), wherein the secondary structure measurement value corresponding to the primary structure of a predetermined protein and the primary structure Prediction accuracy judgment results (60) obtained by comparing each predicted secondary structure predicted value of the plurality of types of prediction simulation programs (11 A, B) are stored in association with the primary structure. Judgment result database (15) and prediction target protein given from judgment result database (15) A search unit (22) for searching a primary structure similar to the primary structure and displaying corresponding determination result data.

(Operation)

Secondary structure measurement value created by comparing the primary structure measurement value and the tertiary structure of the known protein measured by the analyzer, and the secondary structure predicted as the input of the prediction simulation program 11 with the primary structure measurement value The predicted value is compared with each other in the order of the primary structure sequence, and the match / mismatch is determined, and the determination results are aggregated to obtain the overall prediction accuracy (determination result), and the determination result data is converted to the primary structure data. Correspond and make a database.

The search unit 22, when the primary structure data is given, searches the determination result database 60 for a similar primary structure,
The judgment result data is displayed.

As a result, the user can display the prediction accuracy information (judgment result data 60) for the primary structure similar to the primary structure to be predicted, and the prediction simulation programs 11 of multiple types provided in the simulation system can be used. , It is possible to select a highly accurate program and execute the prediction.

〔Example〕

 An embodiment of the present invention will be described with reference to the drawings.

This embodiment shows an example in which the operator selects the prediction simulation program 11, sequentially inputs the primary structure data 51, and collects the judgment results for the prediction simulation program 11 to create a database.

FIG. 2 is a block diagram of a simulation system of the embodiment, FIG. 3 is a flow chart of determination and file processing, FIG. 4 is a flow chart of display processing, and FIG. 5 is a display example of determination results. FIG. 9 is a diagram showing a display example corresponding to the primary structure, and (II) is a diagram showing a display example corresponding to the prediction program.

In the simulation system shown in FIG. 2, 10 is a program file in which a plurality of types of prediction simulation programs 11 are stored, 11 is a plurality of types of prediction simulation programs, 13 is a main memory, and a selected prediction simulation program 11 , 14 is the measured value database, for the known protein, the secondary structure measured value 52a made based on the primary structure measured value and the known tertiary structure is collected for the analyzed protein, Reference numeral 15 is a determination result database, which will be described later on determination result data 60b (hereinafter, the determination result data of the determination unit 16 is a reference numeral 60a,
The judgment result data in the judgment result database is stored as reference numeral 60b), and 16 is a judgment unit, which is a secondary structure measurement value corresponding to the primary structure measurement value of the same structure as the input primary structure data 51. 52a is extracted from the measured value database 14 and the accuracy is determined by comparing the predicted secondary structure predicted value 52b with the predicted output 52b to determine the accuracy, and 17 is the main control unit that determines the operation input and functions of each unit. What is controlled, 18 is an operation unit, which has an input unit and a display unit, 19 is a display control unit, which is the determination result data 60a output from the determination unit 16 and the determination result retrieved from the determination result database 15. Data 60b is displayed on the operation unit 18, and 20 is a judgment result database unit, which edits a series of judgment result data 60a to generate a judgment result database 15, and also a predetermined judgment result data 60 by a search instruction.
Reference numeral 21 is a search file for searching b, and reference numeral 21 is a work file for storing determination result data 60a during a series of determination processes.

As shown in FIG. 5, the secondary structure data 52b of the prediction result shows which secondary structure each amino acid residue of the primary structure data 51 belongs to, in order of sequence, and is expected to belong to, for example, a helix structure. When it is done, it is indicated by a symbol H, when it is expected that it belongs to the sheet structure, it is indicated by a symbol S, and when it is a folded portion, it is indicated by T.

Known secondary structure measurements 52a in the measurements database 14
Is also shown in the same manner, and whether these codes match or not is determined corresponding to the primary structure data 51.

When the determination instruction input, the prediction simulation program selection input, and the primary structure data input are input to the simulation system having the above configuration, the following processing is performed.

(1) The main control unit 17 loads the instructed prediction simulation program 11 into the main memory 13, supplies the primary structure data 51, and starts it.

(2) Loaded prediction simulation program
The prediction process is performed by 11, and the secondary structure prediction value 52b is output.

(3) The determination unit 16 determines the corresponding secondary structure measurement value from the measurement value database 14 based on the input primary structure data 51.
52a is called, and the secondary structure predicted value 52b is compared with each other in the order of sequence to determine whether they match.

(4) The total accuracy is calculated by totaling the coincidences and disagreements.

(5) Secondary structure prediction value corresponding to the primary structure data 51
Each of the data 52b, the secondary structure measured value 52a, and the prediction accuracy is displayed as the determination result data 60a and is stored in the work file 21.

(6) Input different primary structure data 51 and repeat the above process.

(7) The determination result database unit 20 extracts a plurality of determination result data 60a from the work file 21 according to the database creation instruction, and edits the determination result data 60b corresponding to the prediction simulation program as shown in FIG. 5 (II). Then, the judgment result database 15 is generated.

(8) Select another prediction simulation program 11 and perform the above processing.

As a result, the determination result database 15 corresponding to the primary structure data of the data content as shown in FIG. 5 (I) is generated.

If a function of sequentially selecting the predictive simulation program 11 and the primary structure data provided in the simulation system is provided, a database of determination result data can be automatically constructed.

(Display processing) (1) Protein name similar to the primary structure of the prediction target,
Alternatively, the predictive simulation program 11 is designated and a search instruction is given.

(2) The determination result database unit 20 extracts predetermined determination result data 60 from the determination result database 15, and the display control unit 19 uses the operation unit 18 in a format as shown in FIGS. 5 (I) and (II). To display.

As described above, by providing the plurality of types of prediction simulation programs 11, the measurement value database 14, the determination unit 16, and the determination result database unit 20, the prediction accuracy information for each prediction simulation program 11 can be converted into a database. This makes it easy for the user to select the prediction simulation program 11 suitable for the primary structure of the prediction target by looking at this determination result.

〔The invention's effect〕

INDUSTRIAL APPLICABILITY The present invention provides a simulation system of a protein secondary structure that includes a plurality of types of prediction simulation programs and acquires and displays preliminary accuracy information. Therefore, the effect of enabling accurate and rapid prediction is extremely large. .

[Brief description of the drawings]

FIG. 1 is a principle diagram of the present invention, FIG. 2 is a block diagram of a simulation system of an embodiment, FIG. 3 is a flowchart of determination and file processing, FIG. 4 is a flowchart of display processing, and FIG. 5 is a table of determination results. FIG. 6 is a diagram showing an example, (I) is a diagram showing a display example corresponding to a primary structure, (II) is a diagram showing a display example corresponding to a prediction program, and FIG. 6 is a structural analysis procedure explanatory diagram of a protein. In the figure, 10 is a simulation program file, 11 is a simulation program, 13 is a main memory, 14 is a measurement value database, 15 is a judgment result database, 16 is a judgment section, 17 is a main control section, 18 is an operation section, and 19 is a display. Control unit, 20 determination result database unit, 21 work file, 22 search unit, 51 primary structure data, 52a secondary structure measured value, 52b secondary structure predicted value, 60 determination result data, 60a Is the discrimination result data output by the discrimination unit 16, and 60b is the discrimination result data stored in a database.

Claims (1)

(57) [Claims] 1. A protein secondary structure simulation system for selecting a predictive simulation program adapted to a protein to be predicted from a plurality of types of predictive simulation programs for predicting secondary structure from the primary structure of a protein. The determination result of the prediction accuracy obtained by comparing the secondary structure measurement value corresponding to the primary structure of the protein and each secondary structure prediction value of the plurality of types of prediction simulation programs predicted for the primary structure A determination result database stored in association with the structure; and a search unit that searches the determination result database for a primary structure similar to the primary structure of the predicted protein and displays the corresponding determination result data. , Secondary structure measurements of known protein primary structures and multiple species The prediction accuracy judgment obtained by comparing the predicted secondary structure values predicted by each of the prediction simulation programs is stored in a database, and the prediction accuracy of the primary structure similar to the primary structure of the protein to be predicted is displayed to predict the simulation. A protein secondary structure simulation system characterized by allowing a program to be selected.