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
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[0026] Example 1:
[0027] (1) Obtain the protein structure code 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, and dissolve it into a rectangular water box (Water Box) filled with 0.9% NaCl solution, and make the minimum distance from each wall of the water tank 10 , The peptide-salt solution system was obtained, and the system was made into a structure containing non-hydrogen atom position data, named 1o4x_ionized.pdb, and the system was made into a structure containing hydrogen atoms and hydrogen bond parameters, named 1o4x_ionized.psf ;
[0029] (3) Using NAMD_2.6_Linux-i686 software, using the Charmm27 force field, using the Steepest Descent method, under the periodic boundary conditions (Periodic Boundary Conditions PBC), the total time length of the above peptide-salt solution system is 20 picoseconds (ps Minimize the energy of ). In this process...
Example Embodiment
[0036] Example 2:
[0037] (1) Obtain the protein structure 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, and dissolve it into a rectangular water box (Water Box) filled with 0.9% NaCl solution, and make the minimum distance from each wall of the water tank 10 , The peptide-salt solution system was obtained, and the system was made into a structure containing non-hydrogen atom spatial position data, named 1JLU_ionized.pdb, and the system was made into a structure containing hydrogen atoms and hydrogen bond parameters, named 1JLU_ionized.psf ;
[0039] (3) Using NAMD_2.6_Linux-i686 software, using the Charmm27 force field, using the Steepest Descent method, under the periodic boundary conditions (Periodic Boundary Conditions PBC), the total time length of the above peptide-salt solution system is 20 picoseconds (ps ) Energy minimization (Minimize) ...
Example Embodiment
[0046] Example 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, and dissolve it into a rectangular water box (Water Box) filled with 0.9% NaCl solution, and make the minimum distance from each wall of the water tank 10 , The peptide-salt solution system is obtained, and the system is made into a structure containing non-hydrogen atom spatial position data, named 1HN2_ionized.pdb, and the system is made into a structure containing hydrogen atoms and hydrogen bond parameters, named 1HN2_ionized.psf ;
[0049] (3) Using NAMD_2.6_Linux-i686 software, using the Charmm27 force field, using the Steepest Descent method, under the periodic boundary conditions (Periodic Boundary Conditions PBC), the total time length of the above peptide-salt solution system is 20 picoseconds (ps ) Minimize the energy. In this proce...
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