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Computing method for processing interaction between small molecules and proteins

A computational method and protein technology, applied in the field of computational toxicology, can solve problems such as human damage, inability to combine functional molecules, and changes in protein secondary structure content, and achieve the effects of simple key principles, improved production efficiency, and easy learning

Inactive Publication Date: 2013-04-17
TONGJI UNIV
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

Under normal circumstances, the presence of pollutants will affect the changes in the secondary structure content of proteins; secondly, the active sites of proteins are occupied by pollutants, and some functional molecules cannot be combined, resulting in some critical effects on human health. The substances cannot be synthesized or transformed, and the human body will eventually be damaged due to the lack of these important substances that should be synthesized

Method used

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Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0024] The present invention is divided into two functional modules, Presearch and SearchProtein. It is mainly written in ANSI C++ language and can run under Windows and Linux operating systems. There are 18 source programs and header files in the package. The main process is: reading of receptors and ligands, mainly in mol2 file format; preprocessing of receptors and ligands, mainly atom types, uniaxial rotatable key assignment, etc. The PreSearch program needs to prepare the presearch.txt file before running; then randomly initialize the small molecule, and the initialization position of the small molecule is around the active center Randomly generated within the range; then use Presearch for search and docking calculations. The RMSD (root mean square offset) of the docking, the docking free energy ΔG and the coordinates of the docking site were calculated. Establish a protein database, and use the SearchProtein module to perform reverse docking experiments on small mole...

Embodiment 2

[0028] A method to find the protein receptors that PFOS may interfere 4D catalytic domain, urokinase catalytic domain, type II carbonic anhydrase, and type IV dipeptidyl peptidase, and briefly analyzed PFOS at the active site of these proteins. The specific process is as follows:

[0029] The PreSearch program needs to prepare the presearch.txt file before running.

[0030] . / PreSearch -p presearch.txt -l result.log -o energy.txt

[0031] It was calculated 10 times during the work to make the evaluation of energy more even. 1a2c.mol2 and 1a2c-l.mol2 represent the mol2 file for the protein and the mol2 file for the ligand, respectively. After completing the calculation of 1 protein, the program will generate the result.log file and the energy.txt file. The result.log file details the docked RMSD (root mean square offset), docking free energy, and the coordinates of the docking site.

[0032]The free energy ΔG for each docking (the last column represents the energy lost due...

Embodiment 3

[0037] A method to study the interaction mechanism of pollutant 2,4-d with human serum protein HAS, as mentioned in Example 1, using the docking program PreSearch to find out that 2,4-D may replace androgens and estrogens The position on HSA interferes with the transport of these two hormones in the human body and affects its normal function, which may cause the imbalance of sex hormones in the body, and the possibility that 2,4-D has an impact on the transport of thyroxine on serum proteins very small.

[0038] We used the docking results of Presearch to analyze the effect of three molecules with similar results, 2, 4-D, estrogen, androgen and HSA after docking. The active center selected for docking is the IIA active site. It is worth mentioning that, When calculating the binding free energies of 2, 4-D and HSA repeatedly, a special phenomenon was found when docking with other molecules. The calculated docking free energy values ​​converged with two Instead of one value, th...

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Abstract

The invention relates to a computing method for processing interaction between small molecules and proteins. The method includes the following steps that (1) ligand file data of the proteins and the small molecules are read in; (2) atom types in ligands of the proteins and the small molecules are judged; (3) positions and angles of the ligands of the small molecules are randomly initialized; (4) a search protein algorithm is operated, coordinates and angles of the ligands of the small molecules are optimized, and a chemscore formula serves as an evaluation function; (5) the computing is ended after maximum iterative times are achieved; and (6) results such as root mean square deviation (RMSD), binding free energy delta G and coordinates of a binding site are analyzed and output. Compared with computing methods for processing the interaction between the small molecules and the proteins in prior art, the computing method for processing the interaction between the small molecules and the proteins has the advantages that when pollutants and biomacromolecules are interacted can be rapidly determined, and the like.

Description

technical field [0001] The invention relates to the field of computational toxicology, in particular to a computational method for processing the interaction of small molecules and proteins. Background technique [0002] With the increasing development of human society, the environmental problems faced by human beings are becoming more and more serious. Various industrial and agricultural waste water, waste gas and waste residue are discharged into the public environment where human beings live. These "three wastes" often contain many compounds that are harmful to human body. At present, many countries and regions in the world have restricted and prohibited the discharge of "three wastes", strictly limited the content of pollutants in the environment, and formulated relevant legal norms to protect the human body from its harm. The process of pollutants causing damage to the human body is the process that pollutants enter the body and combine with some important proteins in ...

Claims

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Application Information

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IPC IPC(8): G06F19/12
Inventor 管翀赵国华曹同成黄晓峰张莹莹
Owner TONGJI UNIV
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