CN101122933A - Method for calculating force between protein and DNA by computer simulation - Google Patents
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Abstract
The invention discloses a method of computing the interactive force between proteins and DNA through computer simulating. In the method, the NAMD_2.6 computing software and the VMD-1.8.6 analysis software are used for molecule dynamics simulation: firstly the protein structure in the PDB database is made into an appropriate research system, then the system is treated for energy minimization, and when the system is heated to the preset temperature, the system is treated for multi-stage balancing; then molecule dynamics simulation is carried out for the system, the target research objects in the system are marked, SMD simulation is carried out for the system, and finally data are processed and analyzed to acquire change of the interactive force between proteins and DNA, and to calculate the maximum interactive force. The method is characterized by wide range of test objects, easy preparation of experimental material, low requirements to devices, high utilization rate, easy and widely application in the fields of life science, physical chemistry and medicine related to molecule identification and gene representing behaviors.
Description
Technical field
The present invention relates to a kind of method of utilizing interaction force size between computer Simulation calculation protein and the DNA, relate in particular to the method for interaction force between a kind of NAMD_2.6 of utilization and VMD-1.8.6 software quantitative examination protein and the DNA.
Background technology
It is the committed step of vital movement process that protein and DNA interact, as transcription factor to DNA go up specific site identification, start or close transcribing of certain specific gene, the duplicating etc. of regulating DNA.Conventional experimental technique adopts the assaying reaction equilibrium constant to detect bond strength between protein and the DNA, also can pass through atomic force microscope, and unimolecule is operated, and protein and DNA is split up into dissociation process information is provided.But because experiment material is difficult to preparation, be the assaying reaction equilibrium constant or operate the size that all can not well disclose interaction force between protein and the DNA, and the method for molecular dynamics simulation can remedy above-mentioned deficiency with atomic force microscope.Moreover, can also obtain many important dynamics parameters in protein and the interactional detailed process of DNA (movement locus of each atom) and this process by molecular dynamics simulation.
From McCammon J.A. in 1977 etc. so far first with the method research protein of molecular dynamics, the computing method of molecular dynamics simulation develop rapidly, the yardstick of the system of simulation from the yardstick of hundreds of initial several psecs of atom to more than 260 ten thousand an atom hundreds of nanosecond of today, the object of simulation comprises protein, DNA, RNA etc., and range of application relates to the various fields of pharmacy and life science.But, thereby utilize NAMD_2.6 software for calculation and VMD-1.8.6 analysis software to calculate the method for interaction force size each other by protein and DNA are carried out molecular dynamics simulation, do not appear in the newspapers both at home and abroad at present.
Summary of the invention
At the deficiencies in the prior art, the problem to be solved in the present invention provides a kind of NAMD_2.6 of utilization software for calculation and VMD-1.8.6 analysis software (http://www.ks.uiuc.edu/Research/namd/) thereby calculates the method for interaction force size between them by the molecular dynamics behavior of simulated albumin matter and DNA.
Method of the present invention, carry out as follows:
(1) obtains to contain structured data document from the PDB database by protein and compound that DNA forms;
(2) utilize VMD-1.8.6 software to extract the target protein and the dna segment of desire research, it is dissolved in the rectangular parallelepiped water tank (Water Box) that fills 0.9%NaCl solution, obtain protein-DNA-salt solusion system; The structure that contains the non-hydrogen atom spatial position data in the described system, called after ionized.pdb contains the structure of hydrogen atom and hydrogen bonding parameter, called after ionized.psf;
Wherein: above-mentioned water tank inside dimension is 12 with protein and dna segment apart from the minor increment of each wall of water tank, and protein can move along DNA-protein barycenter line direction and is no less than 50 and is as the criterion;
(3) utilize NAMD_2.6 software, adopt the Charmm27 field of force, with Steepest Descent method, under periodic boundary condition (Periodic Boundary Conditions PBC) above-mentioned protein-DNA-salt solusion system being carried out T.T. length is that the energy minimization (Minimize) of 100 psecs (ps) is handled, per 1 femtosecond (fs) calculating is the centre of sphere with each atom once in this process, radius is the Van der Waals force of other interior this atom of atom pair of the diameter of Spherical Volume of 10 , and it is the centre of sphere with each atom once that per 2 femtoseconds (fs) calculate, radius is the electric field force of other interior this atom of atom pair of the diameter of Spherical Volume of 12 ;
(4) use 20kcal/mol
2The alpha-carbon atom (CA atoms) of harmonious effect of contraction (Harmonic Constraint) constraint protein, and use 10kcal/mol
2Harmonious effect of contraction constraint DNA skeletal atom (nucleic backboneatoms), adopt with step (3) in the identical field of force, periodic boundary condition, Van der Waals force and electric field force computing method, and use Langevin dynamics (Langevin Dynamics) temperature control method and Nose-Hoover Langevin piston pressure control method that temperature is controlled at 280K-320K, pressure is controlled at 1atm, system after step (3) energy minimization handled heats 100 psecs (ps), system is heated up gradually and is stabilized to 280K-320K;
(5) to the system after step (4) heating, use 10kcal/mol
2The alpha-carbon atom of harmonious effect of contraction constraint protein, other condition is identical with step (4), carries out the molecular dynamics simulation of 100 psecs (ps);
(6) remove constraint to the alpha-carbon atom of protein, the same step of other condition (4) is carried out the molecular dynamics simulation of 100 psecs (ps) to the system after step (5) simulation;
(7) use 10kcal/mol
2All atoms of each base-pair of two ends of harmonious effect of contraction constraint dna fragmentation, all hydrogen-oxygen bond distance in the fixed system, PME (Particle Mesh Ewald) the grid length of side is set to 1 ± 0.1 , adopt the field of force, periodic boundary condition, Van der Waals force and the electric field force computing method identical, temperature-control pressure-control method, PME long-range electric field force computing method with step (4), system after step (6) simulation is carried out the molecular dynamics simulation of 2-6 nanosecond (ns), make RMSD (the Root Mean Square Distance) value of system be up to the standard;
(8) the DNA skeletal atom in the system of step (7) simulation back being fixed, is SMD (steered molecular dynamics) atom with the alpha-carbon atom of protein, and (SMDk) is set at 0.1-1kcal/mol with the SMD coefficient
2Any number, SMD translational speed (SMDVel) is set at 0.0005 /fs, SMD recording frequency (SMDOutputFreq) is set at 100, other condition is identical with step (7), system after step (7) simulation is carried out the SMD simulation of 100 psecs (ps), obtain the thermodynamic parameter of each measuring point in this process, called after smd.log;
(9), obtain the power of each measuring point, called after ft.dat with VMD-1.8.6 software processes file smd.log;
(10) be that moment of ordinate, each measuring point is the horizontal ordinate mapping with the power of each measuring point, obtain protein is at the uniform velocity drawn back the process power curve over time from the DNA surface, the peak value of ordinate is the maximal phase interreaction force between protein and the DNA in the curve.
In the above-mentioned method of utilizing interaction force between computer mould albuminoid and the DNA:
Temperature control described in the step (4) is preferably 310K;
Simulated time described in the step (7) was preferably for 4 nanoseconds;
SMD coefficient described in the step (8) is preferably 0.7kcal/mol
2
Utilizing method of the present invention to carry out between protein and the DNA calculating of interaction force compares with traditional means of experiment and has obvious superiority:
(1) determination object is in extensive range, relies on non-covalent interaction can both measure in conjunction with the power between the opened protein matter-DNA compound that forms in database;
(2) experiment material is easy to preparation, utilizes suitable software that the crystal structure of protein-DNA compound is handled a little and gets final product;
(3) equipment requirements is low, goes up to calculate at ordinary PC or the group of planes (Cluster) be made up of ordinary PC to get final product, and does not need to buy main equipments such as atomic force microscope;
(4) plant factor height, cpu busy percentage can reach more than 95% under the situation that does not have interference;
(5) be convenient in the life science relevant with the gene expression behavior and physical chemistry and field of medicaments widespread use with molecular recognition.
Description of drawings
Fig. 1 POU
HDDomain and interactional with it dna segment are dissolved in the 0.9%NaCl solution.
POU among the figure
HDDomain and dna segment are positioned at the right side of water tank, and there are enough spaces in the left side for POU in the SMD simulation
HDThe domain motion.Wherein: A is POU
HDDomain, B are and POU
HDThe dna segment of domain interaction.
After Fig. 2 SMD simulation, POU
HDDomain is away from dna segment.
POU among the figure
HDDomain is along DNA-POU
HDBarycenter line direction moves to water tank left side, DNA invariant position.Wherein: A is POU
HDDomain, B are and POU
HDThe dna segment of domain interaction.
Fig. 3 POU
HDStressed situation of change in the domain motion process.
POU when 100ps
HDThe power maximum that domain is subjected to is about 1542pN.
Embodiment
The invention will be further described below in conjunction with embodiment:
Embodiment 1:
(1) obtaining code from PDB database (http://www.rcsb.org/pdb/home/home.do) is the compound data file of 1o4x, called after 1o4x.pdb;
(2) utilize VMD-1.8.6 software to extract the target protein and the dna segment of desire research, it is dissolved in the rectangular parallelepiped water tank (84 *, 70 *, 61 ) that fills 0.9%NaCl solution, obtain protein-DNA-salt solusion system (see figure 1); The structure that contains the non-hydrogen atom spatial position data in the described system, called after 1o4x_ionized.pdb contains the structure of hydrogen atom and hydrogen bonding parameter, called after 1o4x_ionized.psf;
(3) utilize NAMD_2.6 software, adopt the Charmm27 field of force, with Steepest Descent method, under periodic boundary condition (Periodic Boundary Conditions PBC) above-mentioned protein-DNA-salt solusion system being carried out T.T. length is that the energy minimization (Minimize) of 100 psecs (ps) is handled, per 1 femtosecond (fs) calculating is the centre of sphere with each atom once in this process, radius is the Van der Waals force of other interior this atom of atom pair of the diameter of Spherical Volume of 10 , and it is the centre of sphere with each atom once that per 2 femtoseconds (fs) calculate, radius is the electric field force of other interior this atom of atom pair of the diameter of Spherical Volume of 12 ;
(4) use 20kcal/mol
2The alpha-carbon atom (CA atoms) of harmonious effect of contraction (Harmonic Constraint) constraint protein, and use 10kcal/mol
2Harmonious effect of contraction constraint DNA skeletal atom (nucleic backboneatoms), adopt with step (3) in the identical field of force, periodic boundary condition, Van der Waals force and electric field force computing method, and use Langevin dynamics (Langevin Dynamics) temperature control method and Nose-Hoover Langevin piston pressure control method that temperature is controlled at 310K, pressure is controlled at 1atm, system after step (3) energy minimization handled heats 100 psecs (ps), system is heated up gradually and is stabilized to 310K;
(5) to the system after step (4) heating, use 10kcal/mol
2The alpha-carbon atom of harmonious effect of contraction constraint protein, other condition is identical with step (4), carries out the molecular dynamics simulation of 100 psecs (ps);
(6) remove constraint to the alpha-carbon atom of protein, the same step of other condition (4) is carried out the molecular dynamics simulation of 100 psecs (ps) to the system after step (5) simulation;
(7) use 10kcal/mol
2All atoms of each base-pair of two ends of harmonious effect of contraction constraint dna fragmentation, all hydrogen-oxygen bond distance in the fixed system, PME (Particle Mesh Ewald) the grid length of side is set to 1 ± 0.1 , adopt the field of force, periodic boundary condition, Van der Waals force and the electric field force computing method identical, temperature-control pressure-control method, PME long-range electric field force computing method with step (4), system after step (6) simulation is carried out the molecular dynamics simulation of 4 nanoseconds (ns), make RMSD (the Root Mean Square Distance) value of system be up to the standard;
(8) the DNA skeletal atom in the system of step (7) simulation back being fixed, is SMD (steered molecular dynamics) atom with the alpha-carbon atom of protein, and (SMDk) is set at 0.7kcal/mol with the SMD coefficient
2Any number, SMD translational speed (SMDVel) is set at 0.0005 /fs, SMD recording frequency (SMDOutputFreq) is set at 100, other condition is identical with step (7), system after step (7) simulation is carried out the SMD simulation (the results are shown in Figure 2) of 100 psecs (ps), obtain the thermodynamic parameter of each measuring point in this process, called after 1o4x_smd.log;
(9), obtain the power of each measuring point, called after 1o4x_ft.dat with VMD-1.8.6 software processes file 1o4x_smd.log;
(10) be that moment of ordinate, each measuring point is the horizontal ordinate mapping with the power of each measuring point, obtain protein is at the uniform velocity drawn back the process power curve (see figure 3) over time from the DNA surface, the peak value of ordinate is the maximal phase interreaction force between protein and the DNA in the curve, is about 1542pN.
Embodiment 2:
(1) obtaining code from PDB database (http://www.rcsb.org/pdb/home/home.do) is the compound data file of 1wtq, called after 1wtq.pdb;
(2) utilize VMD-1.8.6 software to extract the target protein and the dna segment of desire research, it is dissolved in the rectangular parallelepiped water tank that fills 0.9%NaCl solution, obtain protein-DNA-salt solusion system; The structure that contains the non-hydrogen atom spatial position data in the described system, called after 1wtq_ionized.pdb contains the structure of hydrogen atom and hydrogen bonding parameter, called after 1wtq_ionized.psf;
(3) utilize NAMD_2.6 software, adopt the Charmm27 field of force, with Steepest Descent method, under periodic boundary condition (Periodic Boundary Conditions PBC) above-mentioned protein-DNA-salt solusion system being carried out T.T. length is that the energy minimization (Minimize) of 100 psecs (ps) is handled, per 1 femtosecond (fs) calculating is the centre of sphere with each atom once in this process, radius is the Van der Waals force of other interior this atom of atom pair of the diameter of Spherical Volume of 10 , and it is the centre of sphere with each atom once that per 2 femtoseconds (fs) calculate, radius is the electric field force of other interior this atom of atom pair of the diameter of Spherical Volume of 12 ;
(4) use 20kcal/mol
2The alpha-carbon atom (CA atoms) of harmonious effect of contraction (Harmonic Constraint) constraint protein, and use 10kcal/mol
2Harmonious effect of contraction constraint DNA skeletal atom (nucleic backboneatoms), adopt with step (3) in the identical field of force, periodic boundary condition, Van der Waals force and electric field force computing method, and use Langevin dynamics (Langevin Dynamics) temperature control method and Nose-Hoover Langevin piston pressure control method that temperature is controlled at 280K, pressure is controlled at 1atm, system after step (3) energy minimization handled heats 100 psecs (ps), system is heated up gradually and is stabilized to 280K;
(5) to the system after step (4) heating, use 10kcal/mol
2The alpha-carbon atom of harmonious effect of contraction constraint protein, other condition is identical with step (4), carries out the molecular dynamics simulation of 100 psecs (ps);
(6) remove constraint to the alpha-carbon atom of protein, the same step of other condition (4) is carried out the molecular dynamics simulation of 100 psecs (ps) to the system after step (5) simulation;
(7) use 10kcal/mol
2All atoms of each base-pair of two ends of harmonious effect of contraction constraint dna fragmentation, all hydrogen-oxygen bond distance in the fixed system, PME (Particle Mesh Ewald) the grid length of side is set to 1 ± 0.1 , adopt the field of force, periodic boundary condition, Van der Waals force and the electric field force computing method identical, temperature-control pressure-control method, PME long-range electric field force computing method with step (4), system after step (6) simulation is carried out the molecular dynamics simulation of 2 nanoseconds (ns), make RMSD (the Root Mean Square Distance) value of system be up to the standard;
(8) the DNA skeletal atom in the system of step (7) simulation back being fixed, is SMD (steered molecular dynamics) atom with the alpha-carbon atom of protein, and (SMDk) is set at 0.1kcal/mol with the SMD coefficient
2Any number, SMD translational speed (SMDVel) is set at 0.0005 /fs, SMD recording frequency (SMDOutputFreq) is set at 100, other condition is identical with step (7), system after step (7) simulation is carried out the SMD simulation of 100 psecs (ps), obtain the thermodynamic parameter of each measuring point in this process, called after 1wtq_smd.log;
(9), obtain the power of each measuring point, called after 1wtq_ft.dat with VMD-1.8.6 software processes file 1wtq_smd.log;
(10) be that moment of ordinate, each measuring point is the horizontal ordinate mapping with the power of each measuring point, obtain protein is at the uniform velocity drawn back the process power curve over time from the DNA surface, the peak value of ordinate is the maximal phase interreaction force between protein and the DNA in the curve.
Embodiment 3:
(1) obtaining code from PDB database (http://www.rcsb.org/pdb/home/home.do) is the compound data file of 1hry, called after 1hry.pdb;
(2) utilize VMD-1.8.6 software to extract the target protein and the dna segment of desire research, it is dissolved in the rectangular parallelepiped water tank that fills 0.9%NaCl solution, obtain protein-DNA-salt solusion system; The structure that contains the non-hydrogen atom spatial position data in the described system, called after 1wtq_ionized.pdb contains the structure of hydrogen atom and hydrogen bonding parameter, called after 1wtq_ionized.psf;
(3) utilize NAMD_2.6 software, adopt the Charmm27 field of force, with Steepest Descent method, under periodic boundary condition (Periodic Boundary Conditions PBC) above-mentioned protein-DNA-salt solusion system being carried out T.T. length is that the energy minimization (Minimize) of 100 psecs (ps) is handled, in this process per 1 femtosecond (fs) calculate-inferior be the centre of sphere with each atom, radius is the Van der Waals force of other interior this atom of atom pair of the diameter of Spherical Volume of 10 , and it is the centre of sphere with each atom once that per 2 femtoseconds (fs) calculate, radius is the electric field force of other interior this atom of atom pair of the diameter of Spherical Volume of 12 ;
(4) use 20kcal/mol
2The alpha-carbon atom (CA atoms) of harmonious effect of contraction (Harmonic Constraint) constraint protein, and use 10kcal/mol
2Harmonious effect of contraction constraint DNA skeletal atom (nucleic backboneatoms), adopt with step (3) in the identical field of force, periodic boundary condition, Van der Waals force and electric field force computing method, and use Langevin dynamics (Langevin Dynamics) temperature control method and Nose-Hoover Langevin piston pressure control method that temperature is controlled at 320K, pressure is controlled at 1atm, system after step (3) energy minimization handled heats 100 psecs (ps), system is heated up gradually and is stabilized to 320K;
(5) to the system after step (4) heating, use 10kcal/mol
2The alpha-carbon atom of harmonious effect of contraction constraint protein, other condition is identical with step (4), carries out the molecular dynamics simulation of 100 psecs (ps);
(6) remove constraint to the alpha-carbon atom of protein, the same step of other condition (4) is carried out the molecular dynamics simulation of 100 psecs (ps) to the system after step (5) simulation;
(7) use 10kcal/mol
2All atoms of each base-pair of two ends of harmonious effect of contraction constraint dna fragmentation, all hydrogen-oxygen bond distance in the fixed system, PME (Particle Mesh Ewald) the grid length of side is set to 1 ± 0.1 , adopt the field of force, periodic boundary condition, Van der Waals force and the electric field force computing method identical, temperature-control pressure-control method, PME long-range electric field force computing method with step (4), system after step (6) simulation is carried out the molecular dynamics simulation of 6 nanoseconds (ns), make RMSD (the Root Mean Square Distance) value of system be up to the standard;
(8) the DNA skeletal atom in the system of step (7) simulation back being fixed, is SMD (steered molecular dynamics) atom with the alpha-carbon atom of protein, and (SMDk) is set at 1kcal/mol with the SMD coefficient
2Any number, SMD translational speed (SMDVel) is set at 0.0005 /fs, SMD recording frequency (SMDOutputFreq) is set at 100, other condition is identical with step (7), system after step (7) simulation is carried out the SMD simulation of 100 psecs (ps), obtain the thermodynamic parameter of each measuring point in this process, called after 1hry_smd.log;
(9), obtain the power of each measuring point, called after 1hry_ft.dat with VMD-1.8.6 software processes file 1hry_smd.log;
(10) be that moment of ordinate, each measuring point is the horizontal ordinate mapping with the power of each measuring point, obtain protein is at the uniform velocity drawn back the process power curve over time from the DNA surface, the peak value of ordinate is the maximal phase interreaction force between protein and the DNA in the curve.
Claims (4)
1. method of utilizing interaction force between computer Simulation calculation protein and the DNA, step is:
(1) obtains to contain structured data document from the PDB database by protein and compound that DNA forms;
(2) utilize VMD-1.8.6 software to extract the target protein and the dna segment of desire research, it is dissolved in the rectangular parallelepiped water tank that fills 0.9%NaCl solution, obtain protein-DNA-salt solusion system; The structure that contains the non-hydrogen atom spatial position data in the described system, called after ionized.pdb contains the structure of hydrogen atom and hydrogen bonding parameter, called after ionized.psf;
Wherein: above-mentioned water tank inside dimension is 12 with protein and dna segment apart from the minor increment of each wall of water tank, and protein can move along DNA-protein barycenter line direction and is no less than 50 and is as the criterion;
(3) utilize NAMD_2.6 software, adopt the Charmm27 field of force, with Steepest Descent method, under periodic boundary condition above-mentioned protein-DNA-salt solusion system being carried out T.T. length is that the energy minimization of 100 psecs is handled, to calculate once with each atom be that the centre of sphere, radius are the Van der Waals force of other this atom of atom pair in the diameter of Spherical Volume of 10 for per 1 femtosecond in this process, and it is that the centre of sphere, radius are the electric field force of other this atom of atom pair in the diameter of Spherical Volume of 12 that per 2 femtoseconds calculate once with each atom;
(4) use 20kcal/mol
2The alpha-carbon atom of harmonious effect of contraction constraint protein, and use 10kcal/mol
2Harmonious effect of contraction constraint DNA skeletal atom, adopt with step (3) in the identical field of force, periodic boundary condition, Van der Waals force and electric field force computing method, and use Langevin dynamics temperature control method and Nose-Hoover Langevin piston pressure control method that temperature is controlled at 280K-320K, pressure is controlled at 1atm, system after step (3) energy minimization handled heats 100 psecs, system is heated up gradually and is stabilized to 280K-320K;
(5) to the system after step (4) heating, use 10kcal/mol
2The alpha-carbon atom of harmonious effect of contraction constraint protein, other condition is identical with step (4), carries out the molecular dynamics simulation of 100 psecs;
(6) remove constraint to the alpha-carbon atom of protein, the same step of other condition (4) is carried out the molecular dynamics simulation of 100 psecs to the system after step (5) simulation;
(7) use 10kcal/mol
2All atoms of each base-pair of two ends of harmonious effect of contraction constraint dna fragmentation, all hydrogen-oxygen bond distance in the fixed system, the PME grid length of side is set to 1 ± 0.1 , adopt the field of force, periodic boundary condition, Van der Waals force and the electric field force computing method identical, temperature-control pressure-control method, PME long-range electric field force computing method with step (4), system after step (6) simulation is carried out the molecular dynamics simulation of 2-6 nanosecond, make the RMSD value of system be up to the standard;
(8) the DNA skeletal atom in the system of step (7) simulation back being fixed, is the SMD atom with the alpha-carbon atom of protein, is 0.1-1kcal/mol with the SMD coefficient settings
2Any number, the SMD translational speed is set at 0.0005 /fs, the SMD recording frequency is set at 100, other condition is identical with step (7), system after step (7) simulation is carried out the SMD simulation of 100 psecs, obtain the thermodynamic parameter of each measuring point in this process, called after smd.log;
(9), obtain the power of each measuring point, called after ft.dat with VMD-1.8.6 software processes file smd.log;
(10) be that moment of ordinate, each measuring point is the horizontal ordinate mapping with the power of each measuring point, obtain protein is at the uniform velocity drawn back the process power curve over time from the DNA surface, the peak value of ordinate is the maximal phase interreaction force between protein and the DNA in the curve.
2. the method for utilizing interaction force between computer Simulation calculation protein and the DNA as claimed in claim 1 is characterized in that: the temperature described in the step (4) is 310K.
3. the method for utilizing interaction force between computer Simulation calculation protein and the DNA as claimed in claim 1 is characterized in that: the simulated time described in the step (7) was 4 nanoseconds.
4. the method for utilizing interaction force between computer Simulation calculation protein and the DNA as claimed in claim 1 is characterized in that: the SMD coefficient described in the step (8) is 0.7kcal/mol
2
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| CN106529187B (en) * | 2016-11-25 | 2019-03-08 | 中国科学院计算机网络信息中心 | Embeded atom method calculation optimization method |
| CN106529187A (en) * | 2016-11-25 | 2017-03-22 | 中国科学院计算机网络信息中心 | Optimization method of embedded atom potential calculation |
| CN107330235A (en) * | 2017-05-08 | 2017-11-07 | 华南理工大学 | A kind of molecule power science study method of polypeptide chain self assembling process |
| CN107330235B (en) * | 2017-05-08 | 2020-07-28 | 华南理工大学 | Molecular dynamics research method for polypeptide chain self-assembly process |
| CN111790327A (en) * | 2019-04-09 | 2020-10-20 | 中国科学院化学研究所 | Molecular design method of ice control material |
| CN112071371A (en) * | 2020-08-28 | 2020-12-11 | 武汉大学 | Computer simulation method and device for substances and materials |
| CN112071371B (en) * | 2020-08-28 | 2021-05-04 | 武汉大学 | Computer simulation method and device for substances and materials |
| CN112116948A (en) * | 2020-09-25 | 2020-12-22 | 山东大学 | Simulation analysis method of DNA polyhedron with special branch number |
| CN114611314A (en) * | 2022-03-21 | 2022-06-10 | 福州大学 | Simulation method for regulating tyrosine dipeptide self-assembly structure |
| CN114611314B (en) * | 2022-03-21 | 2024-06-21 | 福州大学 | Simulation method for regulating tyrosine dipeptide self-assembled structure |
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