Compound Search Device Using Lattice Segmentation for Large Molecules
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Solution Overview
Problem
Current methods for determining protein conformation, such as X-ray crystallography and NMR, are time-consuming and limited by the number of bits handled by annealing machines, making it difficult to search for compounds with large molecular weights due to exponential increases in the number of bits required as protein size increases.
Innovation Solution
A device, method, and program that define a lattice space, limit undesirable regions, assign bits to lattice points, and perform simulated annealing to calculate the minimum energy of an Ising model, allowing for the suppression of arithmetic or quantum bits used in searching compounds, thereby enabling the search of compounds with large molecular weights.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Quantity of substance
If the number of amino acid residues to be searched increases, then the molecular weight and complexity of the compound increases, but the number of bits required for the search increases exponentially
Solution Approach 1:
The patent divides the protein chain into multiple segments or regions, and performs conformational search on each segment separately rather than treating the entire protein as one unit. This segmentation reduces the number of bits required for the search while still achieving comprehensive conformational analysis of the complete protein structure.
Solution Approach 2:
The patent introduces a hierarchical dimension to the conformational search process by organizing the search in multiple levels: first determining conformations of individual segments, then combining them to form the complete protein conformation. This dimensional approach transforms an exponentially complex single-level problem into a manageable multi-level process.
2Measurement precision
If conventional methods like X-ray crystallography or NMR are used to determine protein conformation, then accurate three-dimensional structure information can be obtained, but the process takes a long time and requires specific conditions
Solution Approach 1:
The patent performs preliminary conformational analysis on individual protein segments before combining them into the complete protein structure. This preliminary action on smaller units reduces the overall computational time while maintaining accuracy, as each segment can be analyzed independently and in parallel.
Solution Approach 2:
By segmenting the protein into smaller regions for independent conformational analysis, the patent enables parallel processing and reduces the total time required compared to analyzing the entire protein structure as a single unit, while still achieving accurate overall conformation determination.
3Adaptability or versatility
If the search space for protein conformation is expanded to include larger molecules, then more comprehensive compound search is achieved, but the computational burden increases excessively
Solution Approach 1:
The patent enables searching of larger molecules by dividing them into manageable segments that can be processed with limited computational resources. Each segment is analyzed separately and then integrated, allowing the system to handle compounds of arbitrary size without excessive computational burden.
Solution Approach 2:
The patent adds a hierarchical dimension to the search process, organizing computational effort across multiple levels from individual segments to complete molecules. This dimensional organization allows comprehensive search of large compound spaces while distributing computational load to avoid excessive burden at any single level.
Applied Scientific Principles
This section explains which scientific principles are used to turn an abstract innovation direction into a practical engineering solution.
Function Achieved in This Case
This approach reduces the number of bits needed for protein conformation searches, allowing for the efficient determination of stable protein structures and overcoming the limitations of existing technologies by expanding the searchable space without excessive computational burden.
Implementation Method 1
perform simulated annealing to calculate the minimum energy of an Ising model
Data Source
Figure 1~2B
Figure 2C~3C
Figure 3D~3E
AI summary
A device including: a defining unit to define lattice space that is collection of lattices where compound groups are sequentially arranged; a limiting unit; an assigning unit; an arithmetic unit; a judging unit; and a controlling unit to cause the limiting unit to execute expansion of the limited lattice space, the assigning unit to execute assignment of the bits to the lattice points included in the limited lattice space after the expansion, and the arithmetic unit to execute calculation of the minimum energy, in case where the judging unit judges any of the compound groups assigned to the lattice points is arranged on the outermost edge, wherein the device is device for searching the compound, in which the compound groups are linked with one another.