Batch generating method of pharmacophore model

Abstract

The invention provides a batch generating method of a pharmacophore model. The method comprises the steps of automatically downloading a PDB file of a protein complex structure in a PDB database through a computer script, automatically identifying and keeping the protein complex required in the file; calling a chain required for combination of the protein complex from a virtual file database, andconverting the acquired protein sequence to a FASTA format; then obtaining automatic segmentation and recombination information according to adjacent amino acid information and combinable informationbetween different protein chains which are called from the PDB file, thereby forming a new SD file and a PDB file; and finally through self analysis of the script, performing batch generation of the required pharmacophore model, thereby realizing construction of the pharmacophore model between the proteins. The whole operation is finished in a full automatic manner. Furthermore the method is established based on the PDB file data of biology. Furthermore high accuracy and high efficiency are realized in model establishment.

Description

technical field [0001] The invention relates to the field of computer biology, in particular to a batch generation method of pharmacophore models. Background technique [0002] The original concept of pharmacophore was proposed by Paul Ehrlich in the late 19th century, which refers to the molecular framework with essential characteristic atoms for activity. Since 1997, the International Union of Pure and Applied Chemistry has defined pharmacophore: drug molecule and receptor target When it interacts, it needs to produce an active conformation that matches the geometry and energy with the target. [0003] Pharmacophore models consist of several features of a specific 3D pattern, each typically represented as a sphere (although variants exist), with radii determining tolerances for deviations from precise positions. These features can be marked as a single feature or any logical combination consisting of "AND", "OR" and "NOT". [0004] Pharmacophore features are often used a...

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Problems solved by technology

[0005] The computer-based receptor-based virtual screening method for pharmacophore is slow for millions of compound libraries. In addition to the speed factor, the receptor-based virtual screening method seldom considers the influence of protein flexibility, water molecules, Solvation effects, as well as the conformational constraints of ligands, although receptor-based virtual screening methods can provide information on the interaction between ligands and proteins, it is still an unsolvable problem to accurately predict the binding force of proteins and small molecules, and Existing computer scripts are also unable to realize the construction of pharmacophore models between proteins

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