Allele Competitive Response qm/mm Method in Living Systems

A competitive and systematic technology, applied in bioinformatics, instruments, etc., can solve problems such as increased computing costs, inability to fully describe the movement of electrons, and huge computational loads

Active Publication Date: 2019-09-20
BEIJING INSTITUTE OF TECHNOLOGYGY
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Problems solved by technology

However, because it is based on classical mechanics, it cannot fully describe the motion of electrons. Quantum mechanics, which was born at the beginning of the 20th century, can fully describe the motion of electrons. Nowadays, the method of quantum mechanics can be used to accurately calculate the motion of electrons. , but because it requires a large number of and extremely complex integral operations, the result is a huge amount of calculations and a serious increase in computing costs

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  • Allele Competitive Response qm/mm Method in Living Systems
  • Allele Competitive Response qm/mm Method in Living Systems
  • Allele Competitive Response qm/mm Method in Living Systems

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Embodiment Construction

[0034] Using the QM / MM method, the first step is to divide the entire system into three different regions, namely, zone I including the reactive center, zone II around the reactive center, and zone III composed of all other atoms (such as figure 1 Shown):

[0035] Zone I is the key part of the investigation. Because it involves the formation or breaking of chemical bonds, this area needs to be processed by quantum mechanics, so it is also called the QM area. Zone II is the peripheral environment composed of all atoms outside the active center. It does not directly involve the formation of chemical bonds, and generally involves thousands or tens of thousands of atoms, so it is processed by molecular mechanics, so it is also called MM zone. The atoms that do not belong to zone I and zone II are generally called boundary zone (zone III). So the effective Hamiltonian operator of the whole system can be expressed as:

[0036] H eff =Ĥ 0 QM +Ĥ QM / MM +Ĥ MM (1)

[0037] The three ter...

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Abstract

The invention relates to an algorithm for judging living system disease gene reaction rate, in particular to an allele competing reaction QM / MM method in living system. The method comprises the steps that 1, corresponding molecular crystal structure files are downloaded from databases of proteins, nucleic acid and the like, and multiple reasonable molecular structures are selected from the molecular crystal structure files; 2, the energy, electric charge and energy gradient of the MM part are calculated through a Tinker program; 3, the QM part is optimized through a Gaussian98 program; 4, configuration optimization is conducted on the MM part through a Newton program in tinker; 5, proper reaction coordinates are selected; 6, a reaction path is obtained, and calculation is conducted. According to the calculation method, proper therapeutic schemes can be found for genetic diseases such as sickle cell anemia, that is to say, the conditions of enabling a disease gene not to be capable of generating a reaction or enabling the reaction rate to be lower than that of a normal gene are sought. The method is very meaningful for medical science.

Description

Technical field [0001] The invention relates to an algorithm for judging the reaction rate of pathogenic genes in a life system, in particular to a QM / MM method for the competitive reaction of alleles in the life system. Background technique [0002] "Journal of Harbin Normal University". Volume 31, Issue 6, 2015. Research on QM / MM method. In this article, it is pointed out that the molecular dynamics method is one of the more mature simulation methods, which can efficiently simulate and calculate the biological macromolecular system composed of tens of millions of atoms. However, because it is based on classical mechanics, it cannot fully describe the motion of electrons. Quantum mechanics, which was born in the early twentieth century, can fully describe the motion of electrons. Nowadays, the application of quantum mechanics methods can already calculate the motion of electrons accurately. , But because it needs to perform a large number of and extremely complex integration ca...

Claims

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Application Information

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Patent Type & Authority Patents(China)
IPC IPC(8): G16B50/00
Inventor 白杨白羽
Owner BEIJING INSTITUTE OF TECHNOLOGYGY
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