Zinc enzyme docking method based on optimal geometric matching

A geometric and optimal technology, applied to the analysis of two-dimensional or three-dimensional molecular structure, bioinformatics, informatics, etc., can solve the problem of inability to accurately predict the docking position of small drug molecules and zinc enzymes, and the inability to obtain small molecules Docking results with zincase and other issues

Active Publication Date: 2019-08-20
SUN YAT SEN UNIV
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Problems solved by technology

[0004] In order to overcome the existing docking method or software, the present invention cannot accurately predict the direct docking position of the small molecule of the drug and the zinc enzyme, an

Method used

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  • Zinc enzyme docking method based on optimal geometric matching
  • Zinc enzyme docking method based on optimal geometric matching
  • Zinc enzyme docking method based on optimal geometric matching

Examples

Experimental program
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Effect test

Embodiment 1

[0047] like figure 1 Shown, a zinc enzyme docking method based on optimal geometric matching, including the following steps:

[0048] S1: Read the zinc atom coordinates from the protein coordinate file, determine the coordination number that the protein can provide and calculate the coordination number that the small molecule needs to provide;

[0049] S2: Obtain the three-dimensional structure coordinates of the small molecule, and obtain the small molecule file;

[0050] S3: Calculate the charge of the small molecule through the three-dimensional structure coordinates of the small molecule, and obtain the frcmod structure file;

[0051] S4: Obtain the atom type of the small molecule according to the small molecule file, judge the set of coordination atoms provided by the small molecule, and combine the coordination numbers;

[0052] S5: Determine the coordination mode according to the coordination number, calculate the geometric matching factor, and obtain the coordination...

Embodiment 2

[0080] On the basis of Example 1, redock experiments were carried out on 53 zinc proteins. Under the three conditions of ensuring the coordination number, the same coordination atoms and RMSD That is, the correct docking results of the Glide XP algorithm and Autodock4 are 14 and 13 respectively, while the correct docking results of the present invention are 45, and the accuracy is much higher than that of traditional docking software.

[0081] In the specific implementation process, such as image 3 As shown, Fig. a, Fig. e and Fig. i are three crystal structures, respectively corresponding to four-coordination 1zdp, five-coordination 4lxz and six-coordination 1r1j; Fig. b, Fig. f and Fig. The docking prediction results of the corresponding proteins with five and six coordinations, the coordination number and the coordination distance prediction effect are better; Figure c, Figure g and Figure k are Even using the Glide XP algorithm for the docking prediction results of the c...

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Abstract

The invention provides a zinc enzyme docking method based on optimal geometric matching. The method comprises the steps of reading a zinc atom coordinate, determining a coordination number and measuring a to-be-supplied coordination number; acquiring a three-dimensional structure coordinate of a small molecule, calculating the charge of the small molecule, and acquiring a frcmod structure file; acquiring an atom type of the small molecule, determining a coordination atom set which is supplied by the small molecule, and combining a coordination number; acquiring coordination sampling of the coordination atom in the small molecule; acquiring the position sampling of the whole small molecule; calculating binding energy according to position sampling of the small molecule and the frcmod structure file and performing sequencing, thereby obtaining a predicted docking result. According to the zinc enzyme docking method based on optimal geometric matching, an optimal geometric matching principle is utilized and a zinc SLEF force field and an amber-ff99sb force field are used as scoring function for screening and sequencing the predicting results, thereby acquiring an effective predicting result, and accurately predicting the direct docking position between the small molecule of a medicament and the zinc enzyme.

Description

technical field [0001] The invention relates to the technical field of computer-aided drug design, and more specifically, relates to a zinc enzyme docking method based on optimal geometric matching. Background technique [0002] Accurately assessing the binding energy of drug-target complexes is of great significance for the study of drug molecular mechanisms and the development of new drugs. Computer-aided drug design can be realized by molecular docking method, various drug-target interactions can be described, and the small molecule structure of the drug and the prediction of the binding energy of the target can be realized, which can effectively reduce the cost of new drug research and development, and provide support for experimental measurement and clinical trials. forecast and guidance. The molecular docking method mainly involves two main steps of spatial identification and energy evaluation. In terms of spatial recognition, molecular docking algorithms are relativ...

Claims

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Application Information

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IPC IPC(8): G16B15/30
CPCG16B15/30
Inventor 王凯巫瑞波
Owner SUN YAT SEN UNIV
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