Construction method of single ligand residue template library of metal ion binding sites in three-dimensional structure of protein and prediction method based on such single ligand residue template library

Abstract

The invention discloses a construction method of a single ligand residue template library of metal ion binding sites in a three-dimensional structure of protein and a prediction method based on such single ligand residue template library. The construction method develops a new method, in which a naturally existing single ligand residue metal binding state is used as a template, key geometric quantity D, G and C values are used as one of retrieval and screening conditions for whether the template is matched with the potential ligand residues, a search and screening strategy of firstly determining a possible position of the metal by the potential first and second ligand residues and then gradually adding other ligand residues is used, and a final total ordering and screening mode of using a scoring method of calculating confirmation Deviation value between predicted sites and natural and standard sites is provided. Moreover, according to the invention, zinc site prediction is taken as an example, prediction performance of the method is detected, and the method has good prediction effect superior to that of other existing methods.

Description

Technical field [0001] The present invention relates to the fields of bioinformatics, structural biology, and computational biology, in particular to the field of metal site research based on the three-dimensional structure of proteins, and more specifically to a single ligand residue of a metal ion binding site in a three-dimensional protein structure The establishment method of the template library and the prediction method based on it. Background technique [0002] Metalloproteins containing metal ions account for about one-third of the total protein, and they are widely stored in nature and play a variety of biological functions. The metal ion binding site is often the catalytic center of the enzyme or plays an important role in structural stability or regulation. Determining what kind of metal ion, binding site position and how to bind the natural unknown protein can help predict and study the function of the metalloprotein. However, modern molecular biology research often...

AI Technical Summary

Problems solved by technology

There is still a shortcoming, because the TEMSP method predicts the side chain conformation of potential ligand residues based on the template conformation in units of residue pairs, when the number of predicted metal binding site residues is odd, at least one potential ligand residue Two templates are used for side chain conformation prediction, resulting in two side chain conformation prediction structures being output at the same time

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