Calculation method for predicting high-order multi-polar distance of atoms in RNA based on ARDGPR model
A technology of model prediction and calculation method, which is applied in the direction of computational theoretical chemistry, chemical statistics, instruments, etc., can solve the problems of high calculation cost and time-consuming atomic high-order multi-pole distance, and achieve high prediction accuracy, less time and low cost. Inexpensive and easy effect
Active Publication Date: 2020-11-24
LANZHOU UNIVERSITY
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In order to solve the problems of time-consuming calculation of atomic high-order multipole distances by quantum chemical methods and high calculation costs, the present invention proposes a calculation method for predicting atomic high-order multipole distances in RNA molecules based on the ARDGPR model
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[0049] Below in conjunction with example further illustrate the present invention.
[0050] The content of the present invention is to provide a calculation method based on the ARDGPR model to predict high-order multipolar distances of atoms in RNA. Among them, atomic high-order multipole moments include atomic point charges, dipole moments, quadrupole moments, octopole moments, and sixteen pole moments.
[0051] Such as figure 1 Shown, the present invention comprises the following steps:
[0052] First, RNA molecules of different structures and sizes are selected from the protein database (PDB), and the selected RNA molecules are cut into small molecular fragments, where the small molecular fragments include: phosphoric acid molecule, five-carbon sugar molecule, four base molecules (A, C, G, and U), phosphate-five-carbon sugar molecules, four-five-carbon sugar-base molecules, nucleotide molecules and nucleotides... nucleotides. Then, the structures of all small molecule fr...
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The invention relates to a calculation method for predicting the high-order multi-polar distance of atoms in RNA based on an ARDGPR model. The calculation method comprises the following steps: optimizing the structures of all RNA molecule small fragments through quantum mechanics calculation software Gaussian09, and calculating the high-order multi-polar distance of the atoms in the molecule through AIMALL software integration; for each small molecule fragment, selecting the coordinate position of each atom in part of the small molecule fragments and the high-order multi-polar distance of theatom to train an ARDGPR model; and verifying the prediction result of the ARDGPR model by taking the residual small molecular fragment conformation as a test set. According to the method, quantum mechanics calculation is replaced with ARDGPR model prediction, and on the basis of molecular mechanics simulation based on force field information, physicochemical parameter information such as energy, high-order multi-polar distance of atoms and the like can be quickly given for different conformations; the high-order multi-polar distance of atoms is predicted through the trained ARDGPR model, so that the time is short, the cost is low, and the prediction precision is high; and the method is simple and convenient, a large amount of manpower, material resources and financial resources can be saved, and a corresponding basic tool and a corresponding quick way are provided for improving the RNA molecular force field simulation precision.
Description
technical field [0001] The invention belongs to the field of combining quantum mechanics and molecular mechanics calculations, calculation methods and artificial intelligence, and specifically relates to a calculation method for predicting high-order multipole distances of atoms in RNA based on an ARDGPR model. Background technique [0002] RNA analysis is a very important topic in modern analytical science, and it is the basis for interpreting RNA functions and exploring the molecular mechanisms of diseases. The cost of determining the structure of RNA by traditional experimental methods is high, and the molecular state at each moment in the biological process of RNA cannot be observed and recorded, so sufficient information on the secondary structure of RNA cannot be obtained. With the development of interdisciplinary subjects, more and more computer technology is applied to the fields of chemistry and biology to solve the molecular information that is difficult or even im...
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IPC IPC(8): G16C10/00G16C20/70
CPCG16C10/00G16C20/70
Inventor 袁永娜刘振宇
Owner LANZHOU UNIVERSITY