Feature Amount Calculation for Cyclic Peptide Structure Representation
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Solution Overview
Problem
Conventional methods fail to accurately reflect molecular structures with cyclic sequences into feature amounts, particularly in drug discovery applications where molecular structures with specific sequences and cyclic structures are involved.
Innovation Solution
A feature amount calculation program and device that processes structure specifying information to count pairs of atomic groups at specific distances in cyclic molecules, creating a matrix that represents the positional relationships and types of amino acids in cyclic peptides, thereby accurately reflecting the molecular structure in feature amounts.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If conventional feature amount calculation methods are used, then the calculation process is simple, but the accuracy of reflecting cyclic molecular structures is poor
Solution Approach 1:
The patent segments the molecular structure into atomic groups and calculates feature amounts by counting pairs of atomic groups at specific sequence distances. This segmentation allows accurate representation of cyclic structures by breaking down the complex molecular structure into manageable components (atomic groups) and their positional relationships, resolving the contradiction between accuracy and complexity.
Solution Approach 2:
The patent introduces a new dimension of analysis by considering sequence distance between atomic groups in cyclic molecules. Instead of traditional 2D or 3D spatial representations, the invention adds a dimensional aspect that counts pairs at specific distances along the sequence, enabling accurate capture of cyclic structural features while maintaining computational tractability.
2Measurement precision
If detailed structural information is captured, then the feature amount represents molecular structure accurately, but the calculation time increases
Solution Approach 1:
The patent applies partial action by calculating feature amounts for specific pairs of atomic groups at predetermined distances rather than considering all possible pairs or continuous structural analysis. This selective approach captures essential structural information for drug discovery while significantly reducing calculation time compared to comprehensive structural analysis methods.
Solution Approach 2:
The patent changes the parameter of analysis from continuous structural data to discrete count-based features. By transforming structural information into counts of atomic group pairs at specific distances, the method maintains representational accuracy while enabling faster computation through simpler arithmetic operations rather than complex geometric calculations.
3Adaptability or versatility
If cyclic molecular structures are considered, then the feature amount reflects drug discovery requirements accurately, but the complexity of processing increases
Solution Approach 1:
The patent creates a universal feature amount calculation method that handles both cyclic and non-cyclic molecular structures using the same algorithmic framework. The method universally counts pairs of atomic groups at specified distances, which works for any molecular structure type, thereby adapting to drug discovery requirements without requiring separate processing for cyclic molecules.
Solution Approach 2:
The patent simplifies the representation of cyclic molecular structures by creating a copied or abstracted version of the structure in terms of atomic group sequences and pairwise distances. This abstraction captures the essential features of cyclic structures for drug discovery applications while transforming them into a simplified computational representation that reduces processing complexity.
Data Source
AI summary
A computer-readable recording medium storing a feature amount calculation program for causing a computer to execute processing including: receiving structure specifying information indicating a type of each of atomic groups and a sequence of the atomic groups regarding a cyclic molecule in which the atomic groups classified into a plurality of types is cyclically sequenced; specifying an optional first type and an optional second type in the plurality of types; specifying, based on the structure specifying information, one or more of first atomic groups classified into the first type and one or more of second atomic groups classified into the second type out of the atomic groups; and calculating, based on the structure specifying information, a number of pairs of the first atomic group and the second atomic group in which a mutual distance in the sequence between the first atomic group and the second atomic group is a distance.