Protein folding parallel predicting method

Abstract

The invention relates to a protein folding parallel predicting method. The method includes the following steps: obtaining different protein structures through molecular dynamics simulation; setting different temperatures, and obtaining more protein structures with different conformations; partitioning the protein structures with different conformations through a conjugate cap molecule partitioning method, decomposing amino acids from proteins, and wearing a conjugate cap on each amino acid; calculating out the electrostatic potential of molecular fragments through quantum mechanics software to fit out the electric charge of each atom in each amino acid molecular fragment, and updating the electric charge of atoms in a molecule force field. To research protein folding, the scheme of considering a protein polarization effect and a copy interchange-based method are organically integrated, and then two difficult problems of atom interaction potential and a sampling technique in dynamics simulation can be overcome in order to achieve a good effect in protein folding simulation.

Description

technical field [0001] The invention relates to a parallel method for protein folding prediction, which belongs to biological information technology, computing method and computer virtual reality technology. Background technique [0002] The structure of a protein determines its function, and just knowing the genome sequence does not allow us to fully understand the function of a protein, let alone how it works. X-ray diffraction (X-ray diffraction) and nuclear magnetic resonance (nuclear magnetic resonance) are currently the most effective experimental methods for obtaining the three-dimensional structure of proteins. Although there are many crystal structures in the protein crystal database, due to the difficulty of experiments, Many important proteins do not currently have crystal structures. What is more critical is that the function of a protein is not only related to its static structure, but also closely related to its dynamic changes. Research ideas on the function...

AI Technical Summary

Problems solved by technology

[0009] The replica exchange molecular dynamics simulation (REMD) sampling technique is often used in the protein folding process. At present, it has achieved very good results in the conventional small peptide folding process. However, due to the limitation of computing resources, protein Due to the limitation of its own force field, the folds that can be obtained at present are very limited

In addition, the current method of temperature replica exchange also has the following problems: in the actual simulation process, the protein system is in the aqueous solution system, and to obtain a better sampling effect, due to the number of replicas required and the total number of the system The square root of the number of atoms is proportional, so because the number of water molecules is very large, the number of copies required for the simulation basically depends on the number of water molecules, so the amount of calculation required is also greatly increased

In fact, what we focus on is the conformational space of protein molecules. Based on this, we propose a new theoretical calculation model. Through this calculation method, in theory, the number of copies required is only related to the number of atoms in the protein, and not related to the number of atoms in the protein. The number of molecules is independent, so that the number of copies required is greatly reduced, and the conformational sampling effect of the protein we care about is no different from ordinary temperature copy exchange

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