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Method for establishing molecular simulation force filed of protein system

A molecular simulation and protein technology, applied in special data processing applications, instruments, electrical digital data processing, etc.

Inactive Publication Date: 2012-11-14
GRADUATE SCHOOL OF THE CHINESE ACAD OF SCI GSCAS
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Problems solved by technology

Until now there has not been a single successful example of a truly de novo folding α / β protein

Method used

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  • Method for establishing molecular simulation force filed of protein system
  • Method for establishing molecular simulation force filed of protein system
  • Method for establishing molecular simulation force filed of protein system

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Embodiment Construction

[0015] Using the amino acid tetrapeptide chain structure (ACE-ALA-XXX-ALA-NME, XXX=one of 20 amino acids) as a model, we selected five representative structures (right-helical (α R , φ=-57.0, ψ=-47.0), left helical (α L , φ=57.0, ψ=47.0), β-sheet (β, φ=-119.0, ψ=113.0), antiparallel β-sheet (β a , φ=-140.0, ψ=135.0), PPII (PPII, φ=-79.0, ψ=150.0), the selection of the side chain dihedral angle is the same as that of the dipeptide model side chain dihedral angle), and MP2 / cc - The result of pVTZ calculation is used as a standard to check the accuracy of the force field. In order to compare the relative energies of the five configurations of the 20 amino acids with different quantum chemistry and other versions of the AMBER force field method. In the calculation of the density functional method M052x and B3LYP, the configuration of the model molecule is firstly optimized in the gas state using the 6-31G** basis set, and the ASP and GLU models are optimized using the 6-31+G* ba...

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Abstract

The invention relates to a method for establishing a molecular simulation force field of a protein system. For establishing the force field, a tetrapeptide structure of amino acid is taken as a model, five representative structures are selected, and the configuration of the model molecules is as follows: firstly optimizing a gaseous 6-31G**base group, then conducting single-point correcting on gaseous 6-31G**, 6-311++G** and a cc-pVTZ base group, and conducting single-point energy calculation by using the configuration optimized by M052x / 6-31G** through an MP2 / cc-pVTZ method. A water solvent model adopted by liquid-state calculation is IEFPCM, and when a hole is constructed, a UAKS united-atom topology model is selected. The force field is obtained by the method, the accuracy is improved greatly, the calculated RMS (Root Mean Square) value is obviously smaller than that of other force fields, and approaches to the M052x result of a QM method, the calculated RMS-C value indicates that the new force field method overcomes the defect of conformation deviation in the original force field.

Description

technical field [0001] The invention relates to a molecular simulation force field for a protein system. Background technique [0002] Since the inception of molecular mechanics, different computer simulation methods have been developed. For example, the MD method for studying biomolecular dynamics, the docking method for studying the interaction between macromolecules and small molecules, and the Rosetta method for predicting protein structures from scratch. For all these computational simulation methods, the correct description of the interaction between atoms in the research system is the foundation and core, and its accuracy is directly related to the reliability of the simulation results. In principle, we can obtain the interaction between atoms by solving the Schrödinger equation using quantum chemical calculation methods (such as molecular orbitals, density functionals), but it is not possible to solve the Schrödinger equation for a biomolecular system (including the...

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Application Information

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IPC IPC(8): G06F19/12G06F19/16
Inventor 汪志祥姜金良吴春
Owner GRADUATE SCHOOL OF THE CHINESE ACAD OF SCI GSCAS
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