Allele competing reaction QM/MM method in living system

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 response rate of a disease-causing gene in a life system, specifically a QM / MM method for allele competitive response in a life system. Background technique [0002] "Journal of Harbin Normal University". Volume 31, Issue 6, 2015. Research on QM / MM method. It is pointed out in this paper that the molecular dynamics method is one of the more mature simulation methods, which can efficiently simulate 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 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 needs a large number of and extremely complex integral operations, the result is a huge amount ...

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Problems solved by technology

It is pointed out in this paper that the molecular dynamics method is one of the more mature simulation methods, which can efficiently simulate 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 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 needs a large number of and extremely complex integral operations, the result is a huge amount of computation and a serious increase in computing costs. Even in today's best computing environment, it is impossible to perform such large-scale calculations well. This large-scale calculation occupies an important position in the development of many disciplines such as chemistry and biology. In order to efficiently Performing such large-scale calculations can not only obtain accurate results, but also effectively reduce the calculation cost, so a hybrid dynamics calculation method called QM / MM method emerged as the times require, which uses Quantum Mechanics (Quantum Mechanics) , QM) combined with molecular dynamics (Molecular Mechanics, MM), use the QM method to perform accurate calculations on the few atoms contained in the key parts of the biomacromolecular system that need to be carefully observed, while the remaining atoms in the system Some of them are calculated by MM method. This method improves the accuracy of the calculation results and can effectively reduce the calculation cost, so it is being adopted by more researchers

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