A Fast Small Molecule Structure Alignment Method

Abstract

The invention discloses a quick small molecular structure alignment method. The method comprises the steps of reading two to-be-aligned small molecular structure objects, and extracting three-dimensional coordinates and types of all atoms; according to the types of the atoms, extracting corresponding relative atomic mass; by calculating relative atomic mass differences between all atomic pairs from different small molecules, obtaining an initial score matrix, and obtaining initialized alignment information in the initial score matrix by using a greedy algorithm; under the known alignment information, calculating a rotational translation matrix between the coordinates of the aligned atoms, superposing three-dimensional structures of two small molecules by using the matrix to enable the two small molecules to be overlapped as far as possible in a three-dimensional space, obtaining a new score matrix through a three-dimensional coordinate-based scoring function, and then searching for the score matrix by using the greedy algorithm to obtain new alignment information to update the old alignment information; and repeating the previous step until the alignment information cannot be updated or an upper limit frequency of repeating is reached, wherein the final alignment information is an obtained solution.

Description

technical field [0001] The invention relates to the fields of bioinformatics and drug discovery, in particular to a fast small molecular structure alignment method. Background technique [0002] Small molecules are not uncommon in life activities, and they widely exist in a large number of living organisms. Small molecules usually act as ligands of macromolecules (such as proteins) and interact with macromolecules. This interaction is usually manifested as the binding of small molecules to certain specific positions in macromolecules, so that they can cooperate together as Life activities provide specific functions. In addition, drugs often exist in the form of small molecules, and evaluating the similarity between small drug molecules plays a vital role in guiding drug discovery. Therefore, in order to thoroughly understand the process of life activities, especially the details of the interaction between small molecules and macromolecules, and to speed up the process of d...

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Problems solved by technology

[0005] In order to solve the shortcoming of inaccurate similarity information caused by the lack of alignment information of atoms in the above-mentioned existing small molecule similarity measurement methods, the purpose of the present invention is to propose a fast small molecule structure alignment method to provide more similarity information

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