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Biological inverse synthesis method and system combined with AND-OR tree and single-step reaction rule prediction

A technology of biosynthesis and synthetic methods, applied in chemical property prediction, chemical statistics, chemical machine learning, etc., can solve the problems of low actual availability and low efficiency, and achieve the effect of improving actual availability and efficiency

Pending Publication Date: 2022-04-15
WUHAN UNIV
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

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Problems solved by technology

[0005] The present invention proposes a biological retrosynthesis method and system that combines ANDOR tree and single-step reaction rule prediction, searches and selects molecular nodes through ANDOR tree, and predicts metabolic reaction rules that can generate product molecules through a prediction model based on single-step reaction rules , and the AND-OR tree is extended to realize the generation of synthetic paths, which solves the technical problems of low efficiency and low actual usability existing in the methods in the prior art

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  • Biological inverse synthesis method and system combined with AND-OR tree and single-step reaction rule prediction
  • Biological inverse synthesis method and system combined with AND-OR tree and single-step reaction rule prediction
  • Biological inverse synthesis method and system combined with AND-OR tree and single-step reaction rule prediction

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Embodiment 1

[0042] The embodiment of the present invention provides a bioretrosynthesis method combining ANDOR tree and single-step reaction rule prediction, including:

[0043] S1: Select an OR node from the pre-constructed AND-OR tree, and the molecule corresponding to the OR node is used as the product molecule to be predicted. The pre-constructed AND-OR tree contains two types of nodes, namely AND node and OR node , with nodes representing reaction rules, or nodes representing molecules;

[0044] S2: Use the pre-built single-step reaction rule prediction model to predict the k rules that are most likely to synthesize product molecules in the preset rule set to form the rule set Top-k, and assign a value between (0, 1) to each rule The weight value of , wherein, the preset rule set is obtained based on the metabolic reaction construction in the known metabolic reaction data set;

[0045] S3: Expand the constructed AND or tree, including: adding each rule in Top-k as a new AND node to ...

Embodiment 2

[0130] Based on the same inventive concept, this embodiment provides a bioretrosynthesis system that combines ANDOR tree and single-step reaction rule prediction, including:

[0131] The retrosynthetic planning module is used to select an or node from the pre-constructed and-or tree, and the molecule corresponding to the or node is used as the product molecule to be predicted, wherein the pre-constructed and-or tree contains two types of nodes, respectively And nodes and or nodes, and nodes represent reaction rules, or nodes represent molecules;

[0132] The reaction rule prediction module is used to use the pre-built single-step reaction rule prediction model to predict the k rules that are most likely to synthesize product molecules in the preset rule set to form the rule set Top-k, and assign a (0 , 1) a weight value between, wherein, the preset rule set is obtained based on the metabolic reaction construction in the known metabolic reaction data set;

[0133] The AND-OR t...

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Abstract

The invention provides a biological inverse synthesis method and system combined with AND-OR tree and single-step reaction rule prediction, and the method is characterized in that when a target molecule is subjected to inverse synthesis treatment, the inverse synthesis pathway generation of the target molecule is decomposed into multi-step single-step reaction rule prediction. During single-step reaction rule prediction, the substrate molecule of the reaction rule obtained by the previous step prediction is used as the product molecule of the current reaction rule to be predicted. The SMILES sequence of the product molecule is used as input, and the molecular characteristics of the product molecule are calculated in a user-defined manner so as to be compatible with various single-step reaction rule prediction models. And determining a reaction rule according to a prediction result of the model, and performing extension based on an AND-OR tree structure. And finally, finding a potential synthesis route of the target molecule. According to the method, the speed of finding a feasible synthesis pathway is remarkably increased, complex parameters do not need to be manually set, biologists can be assisted in finding potential metabolic pathways more quickly, the experiment cost is reduced, and the experiment efficiency is improved.

Description

technical field [0001] The present invention relates to the technical field of metabolic pathway analysis in biosynthesis, in particular to a bioretrosynthetic method and system combining ANDOR tree and single-step reaction rule prediction, belonging to the application of ANDOR tree and machine learning method in the field of bioretrosynthesis . Background technique [0002] In the 1960s, Corey proposed the concept of retrosynthesis. The core idea is to break down the target molecule into simpler molecules, which can be combined with chemistry to produce it, and iterated until all the desired compounds are commercially available. . The development of chemical retrosynthesis has been very mature so far. Many commercially available software have been developed to help synthesize high-value compounds, but these software hardly consider the principles of green chemistry. , community safety, ecologically harmful raw materials, catalysts, solvents and reagents, products, by-prod...

Claims

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Application Information

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IPC IPC(8): G16C20/30G16C20/10G16C20/70
CPCG16C20/10G16C20/70G16C20/80G16B5/00G16C20/60
Inventor 刘娟张小蕾冯晶
Owner WUHAN UNIV
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