Visual teaching virtual simulation system for protein structure and function associated with disease mechanism
By designing a virtual simulation system to achieve three-dimensional visualization of protein structure and function and its association with diseases, the problem of insufficient interactivity and relevance of traditional teaching tools is solved, thereby improving students' knowledge absorption rate and teaching effectiveness.
Patent Information
- Application Number
- CN202511609708.1
- Authority / Receiving Office
- CN · China
- Patent Type
- Applications(China)
- Current Assignee / Owner
- Filing Date
- 2025-11-05
- Publication Date
- 2026-02-10
AI Technical Summary
Traditional teaching tools cannot effectively achieve three-dimensional visualization, interactive operation, and disease association of protein structure and function, making it difficult for students to understand the mechanism by which domain mutations lead to disease, and lacking an immersive experience and a complete knowledge system.
Design a virtual simulation system for teaching protein structure and function visualization related to disease mechanisms, including a data storage module, a structure call visualization module, a function-disease association module, an interactive operation module, and a teaching evaluation module. Through a data interface, it realizes the synchronous display and interactive operation of protein three-dimensional structure and function-disease information.
It achieves a deep correlation between protein structure and function and disease cases, supports autonomous operation and mutation simulation, improves knowledge absorption rate, adapts to standardized teaching needs, and reduces technical implementation costs.
Smart Images
Figure CN121506264A_ABST
Abstract
Description
TECHNICAL FIELD
[0001] The present application relates to the field of medical education and bioinformatics visualization technology, in particular to a protein structure and function visualization teaching virtual simulation system related to disease mechanism. BACKGROUND
[0002] The structure and function of proteins have a strict correspondence, and changes in their spatial conformation often directly lead to functional abnormalities and thus diseases, which is a core knowledge point in medical education. However, protein structures are microscopic and complex, and traditional teaching mainly relies on two-dimensional pictures, static models, and written descriptions, which have three key defects: first, the abstraction is strong, students have difficulty establishing a direct link between three-dimensional structures and functions, and the understanding of the mechanism of "domain mutation leading to disease" is superficial; second, the interaction is insufficient, existing teaching tools cannot support students to operate protein models and simulate mutation processes independently, making it difficult to achieve immersive learning-by-doing experience; third, the relevance is missing, the teaching content of protein structure, function mechanism, and disease cases is disconnected, making it difficult for students to form a complete knowledge system of "structure-function-disease".
[0003] In the prior art, three-dimensional structure display software such as PyMOL can realize the visualization of protein structure, but such software is a research tool and lacks teaching adaptability: it does not associate function and disease data, and users need to manually query literature to supplement information; the operation is complex and does not meet the simplicity requirements of teaching scenarios; there is no teaching evaluation and task guidance module, and it cannot meet the standardization teaching requirements. While existing medical teaching software focuses on clinical skill simulation, there is no special system developed for the correlation teaching of protein structure and disease mechanism, resulting in a lack of efficient tools in this field and difficulty in meeting the precision needs of medical personnel training. Therefore, we introduce a protein structure and function visualization teaching virtual simulation system related to disease mechanism. SUMMARY
[0004] The main purpose of the present application is to provide a protein structure and function visualization teaching virtual simulation system related to disease mechanism, which can effectively solve the problems in the background art.
[0005] To achieve the above purpose, the technical solution adopted by the present application is:
[0006] A protein structure and function visualization teaching virtual simulation system related to disease mechanism, comprising a data storage module, a structure calling visualization module, a function-disease correlation module, an interactive operation module, and a teaching evaluation module, each module interacts through a data interface, and the specific operation method comprises:
[0007] S1, the data storage module pre-stores protein database, structure coordinate file library, functional mechanism knowledge base and disease association case base, wherein the protein database contains amino acid sequence and classification information, and the structure coordinate file library is adapted to the input format of external three-dimensional structure display software;
[0008] S2, a user initiates a target protein query request through the interactive operation module, and the structure calling visualization module receives the request, calls corresponding structure coordinate files from the data storage module, calls external three-dimensional structure display software through a preset interface, and generates a three-dimensional structure visualization model of the target protein;
[0009] S3, the function-disease association module matches corresponding function description, key domain mechanism and associated disease data from the function mechanism knowledge base and the disease association case base according to the identification information of the target protein, anchors the data with the three-dimensional structure visualization model, and synchronously displays the structure node and the function-disease information;
[0010] S4, the user performs rotation, scaling, domain splitting or mutation simulation operation on the three-dimensional structure visualization model through the interactive operation module, the structure calling visualization module responds to the operation in real time and updates the model display, and the function-disease association module synchronously updates the function analysis and disease mechanism description of the corresponding operation area;
[0011] S5, the teaching evaluation module generates an interactive test task according to the user operation track and a preset examination question bank, collects user answer data and outputs an ability evaluation report, and completes a teaching closed loop.
[0012] Preferably, in the data storage module, the protein database and the structure coordinate file library establish a one-to-one mapping relationship through UniProtKB identifiers, the disease association case base contains pathogenic mutation site coordinates, structure change data after mutation and clinical case abstracts, and all data are attached with literature reference identifiers.
[0013] Preferably, the preset interface of the structure calling visualization module is a command line calling interface or an API interface, the external three-dimensional structure display software is PyMOL, and the module can control PyMOL to realize switching of different display modes, including ball-stick model, cartoon model and surface model, and support high-light coloring display of key domains.
[0014] Preferably, in S3, the anchor point association is that the function-disease association module converts the coordinate information of the function key site and the pathogenic mutation site into spatial anchor points in the three-dimensional structure model, and when the user clicks the anchor point area in the model, the system pops up a structured information card containing function definition, mechanism, mutation influence and associated disease name.
[0015] Preferably, the interactive operation module supports two operation modes:
[0016] The basic mode includes rotation, translation, scaling and display mode switching functions;
[0017] The advanced mode additionally includes domain deletion, amino acid mutation simulation, hydrogen bond display and distance measurement functions, and the operation trajectory is recorded in real time to the teaching evaluation module.
[0018] Preferably, the functional mechanism knowledge base stores information in a hierarchical manner, including the first-level classification "molecular function", the second-level classification "domain function" and the third-level classification "key amino acid function", and each level of classification is associated with the corresponding three-dimensional structure anchor point and disease case data through hyperlinks.
[0019] Preferably, in S4, the implementation process of the mutation simulation operation is that the user selects the target amino acid residue through the interactive operation module and inputs the mutation type, the structure calling visualization module sends a mutation instruction to the external three-dimensional structure display software, updates the model structure, and the function-disease association module synchronously retrieves the pathogenesis data and related disease cases corresponding to the mutation.
[0020] Preferably, the teaching evaluation module includes a question bank unit, a trajectory analysis unit and a report generation unit;
[0021] The question bank unit is classified by knowledge point type, including structure recognition questions, function matching questions and disease mechanism analysis questions;
[0022] The trajectory analysis unit generates operation scores according to the operation frequency and accuracy of the user on the key domains;
[0023] The report generation unit integrates the operation scores and the answer scores, and outputs an evaluation report containing knowledge point mastery and improvement suggestions.
[0024] Preferably, it also includes an experimental task module, which can generate a standardized virtual experiment process, including a complete task chain of "protein structure analysis - function prediction - mutation simulation - disease correlation analysis", and each task node is provided with operation guidance and knowledge point prompts.
[0025] Preferably, the response delay of the structure calling visualization module and the function-disease association module is ≤500ms, and the three-dimensional structure visualization model is Ensure real-time synchronization of user operation and information display.
[0026] Compared with the prior art, the present application has the following beneficial effects:
[0027] 1. Integrated knowledge system: for the first time, the deep correlation between protein three-dimensional structure, functional mechanism and disease cases is realized, the knowledge fragmentation barrier of traditional teaching is broken, and students are helped to build a complete cognitive chain;
[0028] 2. Teaching experience immersion: support autonomous operation and mutation simulation, convert abstract structure function relationship into interactive visual model, significantly reduce learning difficulty and improve knowledge absorption rate;
[0029] 3. Standardized teaching process: built-in experimental tasks and evaluation system, realize the teaching closed loop of "preparation-operation-assessment-feedback", adapt to the demand of large-scale medical personnel training;
[0030] 4. Strong technical adaptability: through interface calling existing mature structure display software, no need to develop visualization engine, reduce technical implementation cost, and strong data scalability, easy to update and iteration. BRIEF DESCRIPTION OF DRAWINGS
[0031] Figure 1 The running method block diagram of the protein structure and function visualization teaching virtual simulation system related to disease mechanism. DETAILED DESCRIPTION
[0032] In order to make the technical means, creative characteristics and purposes and effects realized by the present application easy to understand, the present application will be further described below in combination with specific embodiments.
[0033] The protein structure and function visualization teaching virtual simulation system related to disease mechanism, with reference to Figure 1 , including data storage module, structure calling visualization module, function-disease correlation module, interactive operation module and teaching evaluation module, each module interacts through data interface, the specific running method includes:
[0034] S1, the data storage module pre-stores protein basic database, structure coordinate file library, function mechanism knowledge base and disease correlation case base, wherein the protein basic database contains amino acid sequence and classification information, the structure coordinate file library adapts to the input format of external three-dimensional structure display software;
[0035] S2, the user initiates a target protein query request through the interactive operation module, the structure calling visualization module receives the request, calls the corresponding structure coordinate file from the data storage module, calls the external three-dimensional structure display software through the preset interface, and generates a three-dimensional structure visualization model of the target protein;
[0036] S3, the function-disease correlation module matches the corresponding function description, key domain action mechanism and related disease data from the function mechanism knowledge base and the disease correlation case base according to the identification information of the target protein, anchors the data and the three-dimensional structure visualization model, realizes the synchronous display of the structure node and the function-disease information;
[0037] S4. Users can perform rotation, scaling, domain splitting or mutation simulation operations on the 3D structural visualization model through the interactive operation module. The structural visualization module responds to the operation in real time and updates the model display. The function-disease association module updates the function analysis and disease mechanism description of the corresponding operation area synchronously.
[0038] S5, the teaching assessment module generates interactive test tasks based on the user's operation trajectory and the preset assessment question bank, collects the user's answer data and outputs the ability assessment report, thus completing the teaching loop.
[0039] In the data storage module, the protein basic database and the structural coordinate file library are mapped one-to-one through the UniProtKB identifier. The disease-related case library contains the coordinates of pathogenic mutation sites, data on structural changes after mutation, and clinical case summaries. All data are accompanied by literature citation identifiers.
[0040] The default interface of the structure call visualization module is a command-line call interface or an API interface. The external 3D structure display software is PyMOL. The module can control PyMOL to switch between different display modes, including ball-and-stick models, cartoon models and surface models, and supports the highlighting and shading display of key structural domains.
[0041] In S3, the anchor point association is specifically as follows: The function-disease association module converts the coordinate information of key functional sites and pathogenic mutation sites into spatial anchor points in the three-dimensional structural model. When the user clicks on the anchor point area in the model, the system pops up a structured information card containing the functional definition, mechanism of action, mutation impact, and associated disease name.
[0042] The interactive module supports two operation modes:
[0043] The basic mode includes rotation, translation, scaling, and display mode switching functions;
[0044] The advanced mode additionally includes functions such as domain deletion, amino acid mutation simulation, hydrogen bond display, and distance measurement, and the operation trajectory is recorded in real time to the teaching assessment module.
[0045] The functional mechanism knowledge base stores information hierarchically, including a first-level category of "molecular function", a second-level category of "domain function" and a third-level category of "key amino acid function". Each category is linked to the corresponding three-dimensional structural anchor point and disease case data through hyperlinks.
[0046] In S4, the mutation simulation operation is implemented as follows: the user selects the target amino acid residue and inputs the mutation type through the interactive operation module, the structure call visualization module sends the mutation command to the external three-dimensional structure display software to update the model structure, and the function-disease association module synchronously retrieves the pathogenic mechanism data and related disease cases corresponding to the mutation.
[0047] The teaching assessment module includes a question bank unit, a trajectory analysis unit, and a report generation unit;
[0048] The question bank units are categorized by knowledge point type, including structure identification questions, function matching questions, and disease mechanism analysis questions;
[0049] The trajectory analysis unit generates an operation score based on the user's frequency and accuracy of operations on key structural domains;
[0050] The report generation unit integrates operation scores and quiz scores, and outputs an assessment report that includes knowledge mastery and improvement suggestions.
[0051] It also includes an experimental task module that can generate standardized virtual experimental processes, including a complete task chain of "protein structure analysis - functional prediction - mutation simulation - disease association analysis", and each task node is equipped with operation guidance and knowledge point prompts.
[0052] The response latency of the structure call visualization module and the function-disease association module is ≤500ms, and the 3D structure visualization model... Ensure real-time synchronization between user actions and information display.
[0053] The technical solution of the present invention will be described in detail below with reference to two embodiments. Both embodiments are based on the Windows operating system, the external three-dimensional structure display software is PyMOL, the system development language is Python, and the functions of each module are implemented collaboratively through code.
[0054] Example 1: Basic teaching scenario for "hemoglobin and sickle cell anemia"
[0055] This embodiment is designed for lower-level undergraduate medical students and focuses on teaching the "linkage mechanism between hemoglobin structure and sickle cell anemia". The system is pre-set with corresponding data and teaching tasks, and the specific implementation process is as follows:
[0056] 1. System initialization and data preparation:
[0057] The data storage module pre-stores: the amino acid sequence of hemoglobin (UniProt identifier P68871), a three-dimensional structural coordinate file (PDB format), a functional mechanism knowledge base (including entries such as "hemoglobin's oxygen-carrying function depends on the structure of heme"), and a disease-related case database (including coordinates of the HBS mutation site (Glu6Val) in sickle cell anemia, structural change data, and clinical symptom summaries). The structure call visualization module pre-sets the PyMOL command-line call interface, and the interactive operation module starts in basic mode by default.
[0058] 2. Structural visualization and information association:
[0059] Students input "hemoglobin" into the search box of the interactive module. The system executes steps S2-S3: The structure call visualization module retrieves the PDB file from the data storage module and sends the command "load 1A3N.pdb; show cartoon; color red, chain A; color blue, chain B" to PyMOL via the interface, generating a cartoon model of hemoglobin tetramer, in which the two α chains are marked in red and the two β chains are marked in blue; The function-disease association module matches the data through the P68871 identifier and marks the heme binding site (His92) and HBS mutation site (Glu6) on the model. When the student hovers the mouse over the anchor point, an information card pops up: "Glu6: Glutamic acid at the 6th position of the N-terminus of the β chain, which mutates to valine, causing hemoglobin aggregation and sickle-shaped red blood cells."
[0060] 3. Interactive Operation and Mechanism Demonstration:
[0061] Students switch to advanced mode and perform the "mutation simulation" operation: select the β chain Glu6 residue, enter "Val" in the interactive panel, and the system executes S4: the structure call visualization module sends the command "mutagenesis 1A3N,b / 6,VAL; showsticks,resi 6and chain B". PyMOL updates the model to display the mutated valine residue; the function-disease association module simultaneously pops up a dynamic analysis window, showing "mutation leads to increased hydrophobicity, hemoglobin aggregates with each other when deoxygenated, forming fibrous deposits, reducing the deformability of red blood cells, causing vascular obstruction and anemia", and attaches a comparison diagram of the aggregated fibrous structure model.
[0062] 4. Teaching evaluation and feedback:
[0063] After the operation is completed, the teaching assessment module executes S5: the trajectory analysis unit records the student's accuracy in operating "mutation site location" and "display mode switching" (weight 40%), the question bank unit pushes 3 test questions (such as "In which subunit of hemoglobin is the pathogenic mutation site of sickle cell anemia located?"), and the student's answer score (weight 60%); the report generation unit outputs an assessment report: "Operation accuracy 90 points, answer score 85 points, overall score 87 points, it is recommended to strengthen the review of the knowledge point of 'the effect of protein mutation on polymerization state'", and attaches relevant case links.
[0064] Example 2: Advanced Scientific Research and Teaching Scenarios for "EGFR and Lung Cancer"
[0065] This embodiment is designed for medical graduate students and resident physicians, focusing on research-oriented teaching on "the association between epidermal growth factor receptor (EGFR) structural mutations and targeted therapy for lung cancer." The system supports custom data import and complex operations. The specific implementation process is as follows:
[0066] 1. System initialization and data preparation:
[0067] In addition to pre-storing standard EGFR (UniProt identifier P00533) data, the data storage module also supports users to import custom data through the interactive operation module: a graduate student imported the structural coordinate file of the EGFR mutant (L858R) of a clinical lung cancer patient and the corresponding targeted drug (gefitinib) binding data; the function-disease association module automatically parses the mutation site coordinates in the file and associates them with the built-in "EGFR tyrosine kinase domain function" knowledge base.
[0068] 2. Structural visualization and information association:
[0069] A user initiates a comparison query for "wild-type EGFR vs L858R mutant EGFR". The system executes S2-S3: the structure call visualization module drives PyMOL to generate a dual-window model, displaying the wild-type (PDB: 2GS6) on the left and the mutant (user-imported file) on the right, and sends the command "show surface,kinase domain; color green,wildtype; color orange,mutant" to highlight the kinase domains of both. The function-disease association module anchors the L858R mutation site and pops up an information card: "L858R: located at position 858 of the kinase domain, leucine is changed to arginine, resulting in continuous activation of kinase activity, promoting tumor cell proliferation, and sensitivity to gefitinib."
[0070] 3. Interactive Operation and Mechanism Demonstration:
[0071] The user performs a "drug binding simulation" operation: The user loads the molecular structure file of gefitinib through the interactive operation module and executes the "docking display" command. The system executes S4: the structure call visualization module sends the command "loadgefitinib.pdb; dock 2GS6,gefitinib; showlines,gefitinib", displaying the binding mode of the drug with wild-type EGFR. The user then switches to the mutant model, repeats the operation, and the system displays a comparison of the binding modes of the drug and the mutant. The function-disease association module simultaneously analyzes: "The L858R mutation leads to a conformational change in the EGFR kinase domain, enhancing the binding affinity of gefitinib; therefore, patients with this mutant type have a response rate of up to 70% to targeted therapy," along with an abstract of a clinical research paper (PMID: 32156498).
[0072] 4. Teaching evaluation and feedback:
[0073] Upon completion of the research task, the teaching evaluation module executes S5: the trajectory analysis unit assesses the user's professionalism in "custom data import," "drug docking operation," and "conformation comparison analysis" (weight 60%), the question bank unit pushes an open-ended question "Based on this operation, analyze the structural basis of the L858R mutation enhancing gefitinib sensitivity" (weight 40%), and the report generation unit outputs an evaluation report: "Operational professionalism 95 points, answer score 92 points, overall score 94 points, it is recommended to further study 'the structural mechanism of EGFR T790M drug resistance mutation'", and recommends relevant research tool links.
[0074] The foregoing has shown and described the basic principles, main features, and advantages of the present invention. Those skilled in the art should understand that the present invention is not limited to the above embodiments. The embodiments and descriptions in the specification are merely illustrative of the principles of the invention. Various changes and modifications can be made to the invention without departing from its spirit and scope, and all such changes and modifications fall within the scope of the present invention as claimed. The scope of protection of this invention is defined by the appended claims and their equivalents.
Claims
1. A virtual simulation system for visualizing and teaching protein structure and function in relation to disease mechanisms, characterized in that, It includes a data storage module, a structure call visualization module, a function-disease association module, an interactive operation module, and a teaching assessment module. These modules interact through a data interface. Specific operational methods include: S1. The data storage module pre-stores a protein basic database, a structural coordinate file library, a functional mechanism knowledge base, and a disease-related case library. The protein basic database contains amino acid sequences and classification information, and the structural coordinate file library is adapted to the input format of external three-dimensional structure display software. S2. The user initiates a target protein query request through the interactive operation module. After receiving the request, the structure call visualization module retrieves the corresponding structure coordinate file from the data storage module and calls the external three-dimensional structure display software through the preset interface to generate a three-dimensional structure visualization model of the target protein. S3. The function-disease association module matches the corresponding functional description, key domain action mechanism and associated disease data from the functional mechanism knowledge base and disease association case base according to the identification information of the target protein, and anchors the data with the three-dimensional structure visualization model to realize the synchronous display of structural nodes and function-disease information. S4. Users can perform rotation, scaling, domain splitting, or mutation simulation operations on the 3D structural visualization model through the interactive operation module. The structural visualization module responds to the operation in real time and updates the model display. The function-disease association module synchronously updates the function analysis and disease mechanism description of the corresponding operation area. S5. The teaching assessment module generates interactive test tasks based on the user's operation trajectory and the preset assessment question bank, collects the user's answer data and outputs an ability assessment report to complete the teaching loop.
2. The virtual simulation system for visualizing protein structure and function in relation to disease mechanisms as described in claim 1, characterized in that, In the data storage module, the protein basic database and the structural coordinate file library are mapped one-to-one through the UniProtKB identifier. The disease-related case library contains the coordinates of pathogenic mutation sites, data on structural changes after mutation, and clinical case summaries. All data are accompanied by literature citation identifiers.
3. The virtual simulation system for visualizing protein structure and function in relation to disease mechanisms as described in claim 1, characterized in that, The preset interface of the structure call visualization module is a command line call interface or an API interface. The external 3D structure display software is PyMOL. The module can control PyMOL to switch between different display modes, including ball and stick model, cartoon model and surface model, and supports the highlighting and shading display of key structural domains.
4. The virtual simulation system for visualizing protein structure and function in relation to disease mechanisms according to claim 1, characterized in that, In S3, the anchor point association specifically involves the function-disease association module converting the coordinate information of key functional sites and pathogenic mutation sites into spatial anchor points in a three-dimensional structural model. When the user clicks on the anchor point area in the model, the system pops up a structured information card containing the functional definition, mechanism of action, mutation impact, and associated disease name.
5. The virtual simulation system for visualizing protein structure and function in relation to disease mechanisms according to claim 1, characterized in that, The interactive operation module supports two operation modes: The basic mode includes rotation, translation, scaling, and display mode switching functions; The advanced mode additionally includes functions such as domain deletion, amino acid mutation simulation, hydrogen bond display, and distance measurement, and the operation trajectory is recorded in real time to the teaching assessment module.
6. The virtual simulation system for visualizing protein structure and function in relation to disease mechanisms according to claim 1, characterized in that, The functional mechanism knowledge base stores information hierarchically, including a first-level category "molecular function", a second-level category "domain function" and a third-level category "key amino acid function". Each category is linked to the corresponding three-dimensional structural anchor point and disease case data through hyperlinks.
7. The virtual simulation system for visualizing protein structure and function in relation to disease mechanisms according to claim 1, characterized in that, In S4, the mutation simulation operation is implemented as follows: the user selects the target amino acid residue and inputs the mutation type through the interactive operation module, the structure call visualization module sends the mutation command to the external three-dimensional structure display software to update the model structure, and the function-disease association module synchronously retrieves the pathogenic mechanism data and related disease cases corresponding to the mutation.
8. The virtual simulation system for visualizing protein structure and function in relation to disease mechanisms according to claim 1, characterized in that, The teaching assessment module includes a question bank unit, a trajectory analysis unit, and a report generation unit; The question bank units are categorized by knowledge point type, including structure identification questions, function matching questions, and disease mechanism analysis questions; The trajectory analysis unit generates an operation score based on the user's frequency and accuracy of operations on key structural domains; The report generation unit integrates operation scores and quiz scores, and outputs an assessment report that includes knowledge mastery and improvement suggestions.
9. The virtual simulation system for visualizing protein structure and function in relation to disease mechanisms according to claim 1, characterized in that, It also includes an experimental task module that can generate standardized virtual experimental processes, including a complete task chain of "protein structure analysis - functional prediction - mutation simulation - disease association analysis", and each task node is equipped with operation guidance and knowledge point prompts.
10. The virtual simulation system for visualizing protein structure and function in relation to disease mechanisms according to claim 1, characterized in that, The response latency of the structure call visualization module and the function-disease association module is ≤500ms, and the coordinate error of the 3D structure visualization model is... Ensure real-time synchronization between user actions and information display.