Coarse-Grained Peptide Structure Search Using Ising Cost Functions
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Solution Overview
Problem
Existing methods for searching stable structures of coarse-grained models using only interaction potential between particles fail to achieve accurate results, necessitating an improvement in search accuracy.
Innovation Solution
A search program that calculates and combines cost values from interaction, angle, dihedral angle, repulsion, and attraction potentials to guide the Ising apparatus in finding stable structures of coarse-grained models that satisfy predetermined conditions.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Ease of manufacture
If only interaction potential between coarse-grained particles is used for searching stable structure, then the search method is simple, but the search accuracy is insufficient
Solution Approach 1:
The patent combines multiple potential energy components (interaction potential, angle potential, dihedral angle potential, repulsion potential, and attraction potential) into a comprehensive cost function. This merging of multiple evaluation criteria enables the search to consider various structural factors simultaneously, thereby improving search accuracy while maintaining methodological simplicity through unified cost calculation.
Solution Approach 2:
The patent introduces multiple parameters beyond simple interaction potential, including angle potentials, dihedral angle potentials, repulsion potentials, and attraction potentials. By changing the parameter set from a single interaction potential to multiple structural parameters, the search method achieves higher accuracy in determining stable structures of coarse-grained models.
2Measurement precision
If multiple potential factors are considered for searching stable structure, then the search accuracy is improved, but the calculation complexity increases
Solution Approach 1:
The patent segments the total cost function into distinct components: interaction potential cost, angle potential cost, dihedral angle potential cost, repulsion potential cost, and attraction potential cost. Each component is calculated separately based on specific structural parameters, allowing the system to manage calculation complexity through modular computation while achieving comprehensive evaluation for high search accuracy.
Solution Approach 2:
The patent creates a universal cost function framework that can evaluate multiple structural aspects (interactions, angles, dihedral angles, repulsion, attraction) through a single unified calculation system. This multi-functional approach allows the same computational framework to handle diverse structural parameters, improving accuracy without proportionally increasing overall system complexity.
Data Source
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AI summary
A search program comprising instructions which, when executed by a computer, cause the computer to execute processing including: obtaining a first cost value of a first potential that corresponds to interaction between coarse-grained particles, a second cost value of a second potential that corresponds to an angle and a dihedral angle between the particles, and a third cost value of a third potential that corresponds to repulsion and attraction between the particles; and instructing an Ising apparatus to search for a structure of a coarse-grained model with which a total sum of the first cost value, the second cost value, and the third cost value calculated for an entirety of the coarse-grained model that includes a plurality of particles satisfies a predetermined condition.