Compound Design Program Ring Structure Linker Generation
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Solution Overview
Problem
Conventional compound design techniques often generate chain linkers instead of ring structure linkers, which are less effective in interacting thermodynamically with proteins, limiting the efficiency of low-molecular compound design for protein interaction.
Innovation Solution
A compound design program and method that disposes virtual single atoms to form bonds within specific ranges, executes a cyclization process to create a chemically proper ring structure linker, enhancing the interaction with proteins by constructing molecular skeletons with ring structure linkers.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Reliability
If conventional compound design techniques are used to generate linkers, then chain linkers are produced, but ring structure linkers that provide thermodynamically advantageous interactions with proteins are not generated
Solution Approach 1:
The patent applies preliminary action by pre-defining cyclization conditions and ring structure parameters before the linker generation process. The system预先 sets up rules for forming ring structures during linker construction, ensuring that ring linkers are generated directly rather than requiring post-processing modification of chain linkers.
Solution Approach 2:
The patent changes key parameters of the linker generation process by introducing cyclization conditions that control ring formation. Specific parameters such as ring size, bond angles, and atomic distances are adjusted to favor ring structure formation over chain structures, thereby improving interaction effectiveness while maintaining design efficiency.
2Reliability
If ring structure linkers are generated to improve thermodynamic interaction with proteins, then the complexity of the design process increases
Solution Approach 1:
The patent applies self-service by enabling the design system to automatically generate ring structure linkers through built-in cyclization algorithms. The system self-manages the complex ring formation process by integrating cyclization conditions and structural constraints directly into the linker generation workflow, eliminating the need for separate manual intervention or external tools.
Solution Approach 2:
The patent makes the linker generation process multi-functional by combining both chain linker and ring linker generation capabilities in a single unified system. The same design platform can generate different linker types (chain or ring) based on predefined conditions, reducing overall process complexity by avoiding the need for separate specialized tools for each linker type.
Data Source
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AI summary
A compound design apparatus (100) stably disposes fragments (130, 140) at an active site (121) of a protein (120) disposed on a simulation space. The compound design apparatus (100) disposes a virtual single atom at a position that does not collide with the protein (120), the fragments (130, 140), or a virtual single atom disposed on the simulation space. The compound design apparatus (100) forms a bond when an interatomic distance and an angle formed by the disposed virtual single atom and a virtual single atom in the fragments (130, 140) or another virtual single atom are within predetermined ranges for bond length and bond angle. The compound design apparatus (100) executes a cyclization process when a set of three contiguous atoms including a virtual single atom forming a bond satisfies a cyclization condition under which a chemically proper ring may be formed when a virtual single atom is added to these atoms.