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An rmsd-based multi-feature analysis method for pharmacokinetics results

A molecular dynamics, drug molecule technology, applied in the analysis of two-dimensional or three-dimensional molecular structure, bioinformatics, informatics, etc., can solve the classification error of the results, ignore the characteristics of the compound, and the processing efficiency is low. The method of artificial judgment is subjective. One-sidedness and other problems, to achieve the effect of ensuring accuracy and optimizing the process

Active Publication Date: 2021-03-16
OCEAN UNIV OF CHINA
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  • Application Information

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Problems solved by technology

[0009] 1. When analyzing the results of molecular dynamics, the method of calculating the binding free energy of compound conjugates is generally used, but this method ignores the structural characteristics of the compound and cannot fully reflect the overall binding degree of the target and the compound , has a certain one-sidedness
[0010] 2. Most of the existing methods for evaluating and classifying the results use manual methods for classification based on accumulated experience. The processing efficiency is low and the method of manual judgment has a certain subjective one-sidedness, and there are large errors in the classification of results.

Method used

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  • An rmsd-based multi-feature analysis method for pharmacokinetics results
  • An rmsd-based multi-feature analysis method for pharmacokinetics results
  • An rmsd-based multi-feature analysis method for pharmacokinetics results

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Embodiment 1

[0029] A method for analyzing the results of pharmacokinetics based on rmsd multi-features, the method is specifically as follows:

[0030] 1) Analysis and extraction of molecular dynamics RMSD image features

[0031] Use molecular dynamics software to perform molecular dynamics simulation on the 5V6A target (Middle East respiratory syndrome coronavirus protease-MERS-CoV) and the DrugBank drug molecule database, and use gnuplot to draw the RSMD change image (RMSD image such as figure 1 shown), the overall feature analysis is performed on the RMSD image, and the RMSD (root mean square error) value between each frame of the compound structure and the original structure is calculated, and then the average value of the RMSD in the entire molecular dynamics process is calculated (such as Figure 1 The mean is 0.152026) and the variance (such as figure 1 Variance is 0.001309) as a feature, and then perform fast Fourier transform on the RMSD overall broken line, convert the image in...

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Abstract

The invention relates to a method for analyzing the results of molecular dynamics of drugs based on rmsd multi-features, which belongs to the technical field of molecular dynamics of drugs. The method comprises the following steps: 1) analyzing and extracting molecular dynamics RMSD image features; / Poisson-Boltzmann surface area method to calculate combined free energy and energy decomposition; 3) SVM classification training. The method of the present invention makes drug molecular dynamics more efficient and accurate through RMSD image and molecular mechanics / Poisson-Boltzmann surface area method.

Description

technical field [0001] The invention belongs to the technical field of pharmacokinetics, in particular to a method for analyzing the results of pharmacokinetics based on rmsd multi-features. Background technique [0002] Molecular dynamics is a set of molecular simulation methods. This method mainly relies on Newtonian mechanics to simulate the movement of molecular systems, and samples are taken from systems composed of different states of molecular molecular systems to calculate the configuration integral of the system, and use the structure Based on the results of type integration, the thermodynamic quantities and other macroscopic properties of the system are further calculated. [0003] Molecular dynamics simulation has become a powerful tool and an indispensable research method for studying molecular conformational changes and functional analysis, and is widely used in drug design, life science, chemical engineering, physical science, drug development, material science...

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Application Information

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Patent Type & Authority Patents(China)
IPC IPC(8): G16C10/00G16C20/70
CPCG16C10/00G16C20/70G16B15/30G16B5/00G16B15/00G16C20/30
Inventor 刘昊张志雨徐锡明
Owner OCEAN UNIV OF CHINA