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Method for simulating protein interaction using computer

A computing method and protein technology, applied in computing, special data processing applications, instruments, etc., to achieve the effects of low equipment requirements, accurate and reliable results, and high CPU utilization

Inactive Publication Date: 2007-10-10
SHANDONG UNIV
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

However, most of these molecular dynamics simulation processes are completed on large-scale computers or high-performance computing centers, and the use of NAMD_2.6_Linux-i686 computing software and VMD-1.8.5 analysis software to perform molecular dynamics simulations on PCs is currently the No report outside

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  • Method for simulating protein interaction using computer

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Experimental program
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Effect test

Embodiment 1

[0027] (1) Obtain the protein structure coded 1o4x from the PDB database (http: / / www.rcsb.org / pdb / home / home.do) and name it 1o4x.pdb;

[0028] (2) Use VMD-1.8.5 software to extract the target peptide chain to be studied, dissolve it into a cuboid water box (Water Box) filled with 0.9% NaCl solution, and make the minimum distance from each wall of the water box 10 Ȧ , to obtain the peptide-salt solution system, make the system into a structure containing the spatial position data of non-hydrogen atoms, and name it 1o4x_ionized.pdb, and make the system into a structure containing hydrogen atoms and hydrogen bond parameters, and name it 1o4x_ionized.psf ;

[0029] (3) Utilize NAMD_2.6_Linux-i686 software, adopt Charmm27 force field, use Steepest Descent method, under periodic boundary conditions (Periodic Boundary Conditions PBC), carry on the above-mentioned peptide-salt solution system for a total time length of 20 picoseconds (ps) ) energy minimization (Minimize) process, in ...

Embodiment 2

[0037] (1) Obtain the protein structure with the code 1JLU from the PDB database (http: / / www.rcsb.org / pdb / home / home.do) and name it 1JLU.pdb;

[0038] (2) Use VMD-1.8.5 software to extract the target peptide chain to be studied, dissolve it into a cuboid water box (Water Box) filled with 0.9% NaCl solution, and make the minimum distance from each wall of the water box 10 Ȧ , to obtain a peptide-salt solution system, and make the system into a structure containing the spatial position data of non-hydrogen atoms, named 1JLU_ionized.pdb, and make the system into a structure containing hydrogen atoms and hydrogen bond parameters, named 1JLU_ionized.psf ;

[0039] (3) Utilize NAMD_2.6_Linux-i686 software, adopt Charmm27 force field, use Steepest Descent method, under periodic boundary conditions (Periodic Boundary Conditions PBC), carry on the above-mentioned peptide-salt solution system for a total time length of 20 picoseconds (ps) ) energy minimization (Minimize) process, in wh...

Embodiment 3

[0047] (1) Obtain the protein structure code 1HN2 from the PDB database (http: / / www.rcsb.org / pdb / home / home.do) and name it 1HN2.pdb;

[0048] (2) Use VMD-1.8.5 software to extract the target peptide chain to be studied, dissolve it into a cuboid water box (Water Box) filled with 0.9% NaCl solution, and make the minimum distance from each wall of the water box 10 Ȧ , to obtain the peptide-salt solution system, and make the system into a structure containing non-hydrogen atom spatial position data, named 1HN2_ionized.pdb, and make the system into a structure containing hydrogen atoms and hydrogen bond parameters, named 1HN2_ionized.psf ;

[0049] (3) Utilize NAMD_2.6_Linux-i686 software, adopt Charmm27 force field, use Steepest Descent method, under periodic boundary conditions (Periodic Boundary Conditions PBC), carry on the above-mentioned peptide-salt solution system for a total time length of 20 picoseconds (ps) ) energy minimization (Minimize) process, in which every 2 fem...

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Abstract

A method of utilizing computer to simulate interaction of protein includes preparing protein structure in PDB databank to be proper study system, carrying out energy minimization treatment on said system, heating said system up to set temperature then carrying out multi-step balance treatment on said system, executing molecular dynamic simulation on said system and studying protein amino acid residual base acted as key function in atom movement race and confirmation variation as well as variation process under set conditions.

Description

technical field [0001] The invention relates to a method for simulating protein interaction by computer, in particular to a method for studying interaction between protein transcription factors by using NAMD_2.6 and VMD-1.8.5 software. Background technique [0002] Protein interaction is a key step in the process of life activities, such as the coordinated regulation of multiple transcription factors, protein folding and enzyme synthesis, molecular recognition and signal molecule transduction, immune response, etc. Conventional experimental methods use the determination of reaction equilibrium constants to detect the binding strength between proteins. Atomic force microscopy can also be used to operate on single molecules and separate proteins from each other to provide information for the dissociation process. However, neither the determination of reaction equilibrium constants nor the operation of atomic force microscopy can reveal the non-bonding interactions between prot...

Claims

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Application Information

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IPC IPC(8): G06F19/00G06F19/16
Inventor 时永香连鹏张楠刘洁
Owner SHANDONG UNIV
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