Fusion Sequence Screening for Protein Insertion Site Evaluation
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Solution Overview
Problem
Existing protein structure analysis methods require extensive user effort when analyzing multiple candidate proteins, as they need to be individually processed, leading to a heavy burden in terms of time and cost.
Innovation Solution
A sequence extraction system that generates and evaluates candidate fusion sequences by inserting amino acid sequences into target proteins based on various patterns, predicting their structures, and extracting suitable sequences for three-dimensional analysis.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If protein structure analysis is performed by individual processing of each candidate protein, then structure prediction accuracy is maintained, but user burden and time consumption increase significantly
Solution Approach 1:
The system segments the protein analysis process into distinct functional modules: sequence generation unit that creates candidate fusion sequences, structure prediction unit that predicts three-dimensional structures, and evaluation unit that assesses prediction results. This segmentation allows parallel processing of multiple candidate proteins while maintaining individual analysis accuracy, thereby reducing overall time consumption without sacrificing prediction precision
Solution Approach 2:
The system performs preliminary actions by pre-generating multiple candidate fusion sequences with different insertion patterns before structure prediction. The sequence generation unit creates these candidates in advance based on target amino acid sequences, allowing the structure prediction unit to efficiently evaluate multiple options simultaneously rather than processing them sequentially, thus reducing time loss while maintaining accuracy
2Reliability
If multiple candidate proteins are analyzed individually through biochemical experiments, then reliable structure determination is achieved, but cost and operational burden increase
Solution Approach 1:
The system creates computational copies of candidate proteins through in silico structure prediction rather than requiring physical biochemical experiments for each candidate. The structure prediction unit generates three-dimensional structure models for multiple candidate fusion sequences computationally, allowing reliable structure determination without the operational burden of conducting separate wet lab experiments for each candidate protein
Solution Approach 2:
The evaluation unit serves multiple functions by simultaneously assessing various aspects of candidate fusion sequences including structure prediction quality, insertion pattern effectiveness, and suitability for three-dimensional analysis. This multi-functionality maintains reliable structure determination while reducing operational burden by consolidating multiple evaluation tasks into a single integrated unit rather than requiring separate specialized experiments for each assessment
Data Source
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Figure 3A~3B
AI summary
A sequence extraction system includes a candidate sequence generation unit that generates a plurality of candidate fusion sequences, which are a plurality of candidates for a fusion sequence in which at least one inserted amino acid sequence corresponding to insertion polypeptide is inserted into an entirety or a part of a target amino acid sequence corresponding to a target protein, based on each of a plurality of candidate insertion patterns, which are a plurality of candidates for an insertion pattern for inserting at least one of the inserted amino acid sequence into the entirety or the part of the target amino acid sequence, a structure prediction result acquisition unit that acquires structure prediction result information indicating a result of prediction of a structure of each of a plurality of candidate fusion proteins corresponding to the plurality of candidate fusion sequences respectively, based on each of the plurality of candidate fusion sequences, an evaluation unit that evaluates an insertion site into which the inserted amino acid sequence is inserted, based on the result of the prediction, and a sequence extraction unit that extracts at least one candidate fusion sequence from the plurality of candidate fusion sequences, based on the result of the evaluation.