Expression method of efficient molecular three-dimensional conformation

Abstract

The invention relates to the technical field of computer-aided drug research and development, in particular to an efficient molecular three-dimensional conformation expression method, which comprises the following steps of: A, establishing a basic fragment library auxiliary file; step B, constructing a molecular three-dimensional conformation; step C, recording metadata for generating the three-dimensional conformation of the molecule; and step D, compressing and storing the metadata. According to the method, explicit recording of the three-dimensional coordinates of each atom in each molecular conformation is avoided, the meta information for efficiently restoring the three-dimensional coordinates of each conformation is recorded, and the memory space of the meta information is 100-1000 times smaller than explicit expression of the three-dimensional conformation; and the speed of recovering the three-dimensional coordinates by the meta data is more than one order of magnitude faster than that of the fastest three-dimensional conformation generation algorithm. Therefore, the method breaks through the storage limitation of the molecular three-dimensional conformation of a super-large-scale chemical molecule database, and provides an effective solution for three-dimensional screening of drug molecules.

Description

technical field [0001] The invention relates to the technical field of computer-aided drug research and development, in particular to a method for expressing three-dimensional conformations of highly efficient molecules. Background technique [0002] The interaction between drugs and receptor molecules is a conformational dynamic matching process, and both drugs and receptor molecules undergo a series of important conformational changes. Only the conformation that can be recognized by the receptor and is complementary to the receptor structure can produce a specific pharmacological effect, that is, the pharmacological conformation. Therefore, the interaction between drugs and receptors is realized in three-dimensional space, and the three-dimensional conformational analysis of molecules is the key to the design of drug molecules. With the development of computer chemistry and molecular graphics, the three-dimensional structure simulation of drugs and receptors has become po...

AI Technical Summary

Problems solved by technology

However, since the molecule has a three-dimensional structure with multiple flexible and rotatable bonds, in order to characterize its conformational space, it is necessary to use a large number of conformations (100-1000) as representatives of its conformational space. Therefore, the above display expression using three-dimensional coordinates will occupy Large file storage space, which will face great technical challenges for the conformational space expression of large molecular libraries of tens of millions or more, not only occupying a huge file storage space, but also forming a huge IO bottleneck for data reading and writing

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