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Computer-aided screening method for small molecule target nucleic acid aptamers based on high-performance computing platform and small molecule target nucleic acid aptamers

A high-performance computing and computer-aided technology, applied in the field of molecular biology, which can solve the problems of nucleic acid molecule grabbing target, difficult separation, loss of target sequence, etc.

Active Publication Date: 2021-05-07
BEIJING COMPUTING CENT
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

[0010] The purpose of the present invention is to provide a fast, specific, sensitive, high-throughput computer-aided screening method for small molecule target nucleic acid aptamers based on a high-performance computing platform, which can reduce the complexity and times of screening, greatly save manpower, material resources and The screening success rate is high. Compared with the traditional simple wet experiment screening method, the screening accuracy is higher, the loss of the target sequence is reduced, and the screening is more targeted. , Nucleic acid molecules are difficult to catch targets, and there are many consumables. The complex formed by the small molecule target combined with nucleic acid has little difference in size, mass, and charge properties from the nucleic acid itself. The separation of the two is difficult, which has important research significance and use value

Method used

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  • Computer-aided screening method for small molecule target nucleic acid aptamers based on high-performance computing platform and small molecule target nucleic acid aptamers
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Embodiment 1

[0073] Example 1: If the energy of the target small molecule target is -5Kcal / mol when it binds to the conformation of nucleic acid a, and the energy when it binds to the b conformation is -6Kcal / mol, then it is more stable when it binds to the b conformation than when it binds to the a conformation. This value is generally Below -3Kcal / mol is considered desirable, therefore, in general, the b conformation is desirable.

Embodiment 2

[0074] Example 2: For example, when the target small molecule target binds to the conformation of nucleic acid a, the energy is -5Kcal / mol, and when it binds to the b conformation, the energy is -6Kcal / mol, but the main hydrophobic part in the b conformation is bound to the affinity of the target small molecule target. At the water end, even if the energy of the b conformation is low, the b conformation is not advisable.

Embodiment 3

[0075] Example 3: For example, when the target small molecule target binds to the conformation of nucleic acid a, the energy is -5Kcal / mol, and when it binds to the b conformation, the energy is -6Kcal / mol, but the main hydrophilic part in the b conformation is bound to the target small molecule target The b-conformation has low energy, and the main hydrophilic part in the b-conformation is bound to the hydrophilic end of the target small molecule target. Therefore, the b-conformation is desirable.

[0076] In a specific embodiment of the present invention, the search acceleration engine is used to screen the small molecule target in the small molecule compound library; the search acceleration engine is used to make molecular docking between the target small molecule target and the nucleic acid molecule in the nucleic acid molecule database. Construct an acceleration engine through parallelization technology to accelerate the matching and retrieval of eigenvalues ​​of nucleic a...

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Abstract

The invention provides a computer-aided screening method for small molecule target nucleic acid aptamers based on a high-performance computing platform, and relates to the technical field of molecular biology. Firstly, analyze the structure of the small molecule target, and then screen in the small molecule compound library. If the matching principle is met, it will be used as the target small molecule target for molecular docking with nucleic acid molecules. If the matching principle is not met, the molecular structure can be constructed. , the small molecule target after molecular structure construction is used as the target small molecule target, and molecular docking is carried out with the nucleic acid molecule. If the docking is successful, the nucleic acid molecule is the primary nucleic acid aptamer, which solves the binding site between the small molecule target and the nucleic acid molecule Small molecular weight, weak affinity, difficulty in grasping nucleic acid molecules, many consumables, small differences in size, mass, and charge properties between the complex formed by the small molecule target and the nucleic acid itself, and the difficulty in separating the two.

Description

technical field [0001] The invention relates to the technical field of molecular biology, in particular to a computer-aided screening method for a small molecule target nucleic acid aptamer based on a high-performance computing platform and a small molecule target nucleic acid aptamer. Background technique [0002] Computational biology is a dynamic emerging interdisciplinary subject, which continues to play an important role in current biological research and is also an important tool for elaborating biological mechanism research. Computational biology can complete complex calculation processes based on a large amount of biological data. It is a great intersection of life sciences and non-life sciences, and it is efficient and convenient. It plays an important role in computer-aided design of genes and proteins, comparative genome analysis, biological system models, cell signal transduction and gene regulatory network research, expert databases, and biological software pack...

Claims

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Application Information

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Patent Type & Authority Patents(China)
IPC IPC(8): G16B15/00G16B20/00G16B30/00G16B50/30C12N15/115
CPCC12N15/115C12N2310/16G16B15/00G16B20/00G16B30/00G16B50/30
Inventor 刘书霞赵新颖裴智勇杨杰刘满姣袁寒玉
Owner BEIJING COMPUTING CENT
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