Team:UESTC-Software/Description
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Background
Difficulties increase as synthetic biology networks expand, limiting the possibility to design more complex biology systems. There are challenges at every step of the way, from the characterization of biological elements to the designing and construction of systems. The effective integration of current research results of synthetic biology is a key step to promote its development. We note that most of the current approaches to protein design are de novo synthesis, requiring targeted modifications or resets of amino acid sequences that require corresponding modifications and resets of DNA. The workload of this approach is undoubtedly huge.
In addition, during the first decade of synthetic biology, most of the research focused on single-module design. Integrating different single modules to perform more complex functions is another key. At present, many excellent databases (CATH, SCOP/SCOP2) have detailed and accurate records of protein domain for protein supersecondary structure , and we assume that it may be feasible to study proteins with more complex functions by using domain as a module. At the same time, the research of domain will also play an important role in the development of synthetic biology in the future. The structural domain research can not only provide appropriate bricks for the design of new proteins, but also offer clues to the evolution of life.
Inspiration
Early on, we investigated a number of protein research topics, but we did not find the ideal one. Feeling depressed, we still held activities to seek inspiration once in a while. The inspiration occured in a building block activity in which Zhaochang Yang accidentally installed a mistaken part from another building block on our building block. Surprisingly, their shapes fit perfectly! Then we thought about whether we can use different domains in nature to splice new proteins, just like we do with building blocks.
After that, we brainstormed with PI and targeted the domain of the supersecondary structure of the protein.We looked through 5 years of iGEM software team projects and found that there were few domain-based researches. We realized that this aspect was a problem that we could solve.So we decided to build a shape-based domain taxonomy library, which aims to provide a series of shape-based domain modules and annotations that will inspire iGEMer to design proteins.
At present, researches based on the shape of a large number of domains are still rare. Most of the existing research is based on the sequence (or the shape between a few domains) for comparison and research. However, this traditional method is very unfavorable for a large number of domains with the same shape to be screened and obtained. In the structural domain reorganization, domains with similar shape will be easier to be recombined to obtain proteins with specific functions.
Hence, we put forward CPD3DS, a new comprehensive component database based on the domain shape. CPD3DS adopts feature extraction and clustering methods through which thousands of domains are divided into limited standard types and 3D stereoscopic models of domains are visualized. With CPD3DS, igemers or biologists could conceivably splice a new protein through domain model or maybe draw inspiration for protein design.
Project
Currently, our team has developed practical functions on CPD3DS and planned to develop it further.
CPD3DS integrates CATH and SCOP/SCOP2 in order to provide as comprehensive and detailed structure domain information as possible. At present, we have achieved remarkable results in four aspects: design originality, data integrity, content accuracy and user-friendliness.
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We have initiated domain classification according to the shape of domain through 3Dzd & K-means; |
Through Uniprot, CATH, SCOP/SCOP2 and PDB, we have integrated domain division, related functions and probability combination into our own project website, so as to form a complete system of domain shape division, structure, and function; |
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We used an authoritative database recognized by the synthetic biology community. Their strict review system and supporting materials ensure the accuracy of the content on our website; |
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We strived to make CPD3DS a more integrated and user-friendly database that provides synthetic biologists with long-term, stable data updates and search services. |
How to use it
For individual users, CPD3DS provides diversified services. They can view related information about each type of domain we classified based on shape: such as sequence, 3D model, function, and combination. In addition, it allows users to jump to the database of the data source via a connection.
For the research team, CPD3DS provides data support services. Users could download all data and all models in our database. We also deployed a web application on our server. http://104.168.165.152/
We are committed to providing better data support services for other software teams. The professional team can also use the URL to obtain rich data about our domain. The data provided is authorized, so users do not have to worry about infringement.
