44 results about "Molecular mechanics" patented technology

Ricin A-chain is an N-glycosidase that attacks ribosomal RNA at a highly conserved adenine residue. Crystallographic studies show that not only adenine and formycin, but also pterin-based rings can bind in the ricin active site. For a better understanding of the recognition mode between ricin, and adenine-like rings, the interaction energies and geometries were calculated for a number of complexes. Shiga toxin, a compound essentially identical to the protein originally isolated from Shigella dysenteriae, has an active protein chain that is a homologue of the ricin active chain, and catalyzes the same depurination reaction. The present invention is drawn to identifying inhibitors of ricin and Shiga toxin, using methods molecular mechanics and ab initio methods and using the identified inhibitors as antidotes to ricin or Shiga toxin, or to facilitate immunotoxin treatment by controlling non-specific cytotoxicity.

The invention discloses a novel affinity ligand polypeptide library of immunoglobulin G (IgG) constructed based on a protein A affinity model and an application of a design method. According to a molecular mechanics / Poisson-Boltzmann solvent-accessible surface area method, a key residue of protein A with a higher affinity interaction with human IgG is analyzed and obtained based on the available human IgG-protein A compound structure; the simplified protein A affinity model is constructed; the affinity polypeptide molecule library of the IgG is constructed based on the simplified protein A affinity model. On the basis of the peptide library, an amino acid type represented by X is ascertained by further utilizing an amino acid location method. Then, candidate polypeptides are screened gradually by applying molecular docking and molecular dynamic simulation means. Finally, polypeptide affinity ligand capable of effectively separating and purifying the IgG is ascertained through an affinity chromatography experimental method.

The invention provides a protein-ligand free energy calculating method based on a MM / PBSA model. The method comprises the following steps of respectively acquiring pdb files of a protein and a ligandmolecule; preprocessing the pdb file of the protein by means of a pdb4amber tool, deleting a hydrogen atom which cannot be read by Amber software; for the pdb file of the ligand molecule, converting the pdb format to a mol2 file format by means of an antechamber tool, and correcting the atom type to the atom type of an amber force field; assigning a GAFF force field parameter of the ligand molecule by means of a tleap command; respectively generating a topological file and a coordinate file of the protein, the ligand micromolecule and a protein-ligand micromolecule composite structure by meansof the tleap command through using an AMBER99SB-ILDN molecule force field parameter, and adding a water box and counter ions in the process; performing energy minimizing, heating and molecular dynamics simulation on a simulation system by means of the Amber software; and performing binding free energy calculation based on a molecular dynamics Poisson-Boltzmann surface area model on a molecular dynamics simulating track in a previous step by means of an MMPBSA.py program.

The invention relates to a method for testing a temperature characteristic of a carbon nanometer pipe. The method combines quantum mechanics and molecular dynamics and utilizes the theories like the density functional theory, the electrical conductivity of the carbon nanometer pipe at different temperatures is tested from the molecule level to the atom level, and therefore the temperature characteristic of the carbon nanometer pipe is obtained. From the view of quantum mechanics, the method of molecular dynamics is combined, the actual conditions of the structures of molecules in different environments are simulated through the molecular dynamics firstly, time and labor are saved, then the temperature conductivity of the molecules are calculated through the quantum mechanics, the test result can be obtained rapidly and accurately, and the method is simple and effective.

Descriptors of cohesive interactions in the solid state are calculated from a computational model of a solid state, i.e. from a small cluster of copies of the molecule of interest assembled using a molecular mechanics method. A model for predicting solubility is built using the cohesive interaction descriptors along with other descriptors useful for this purpose. Predicted solubility is computed for the compound of interest by computing the same descriptors and applying the solubility model. Explicit modeling of solid state allows to more accurately characterize cohesive interactions in solids, hence, more accurately predict solubility.

A method of comparing two conformers in which an overlay score is obtained, comprises providing a set of field points representing field extrema of a first molecule, wherein each field point has a position and a field size value; determining at the position of each of the field points of the first molecule the field of a second molecule to obtain a set of field sample values; and combining the field sample values with the field size values to obtain a score indicative of the field similarity of the first molecule to the second molecule. The method overcomes a limitation of conventional pseudo-Coulombic scoring in which a low score is achieved when extrema of large extent overlap but have their minimum points widely separated. The method can be applied to molecular mechanics modeling using atom centered charges (ACCs) and extended electron distributions (XEDs) as well as to quantum mechanics models.

The invention relates to an efficient implementation method of single-molecular mechanical test, comprising the steps of enabling a sample cell to move relative to light traps through an actuator, andcapturing microspheres; processing in real time to monitor the double light traps until each light trap contains only single microsphere; stopping the actuator operating, controlling a displacement table to drive the sample cell to do simple harmonic motion in the horizontal direction under certain frequency and amplitude; performing single-molecular mechanical test and storing data; when it is monitored that each light trap contains no single microsphere and if multiple microspheres occur in the light trap, controlling a retaining plate to close and then open to release the microspheres fromthe light traps, controlling a piezoceramic mirror PM to rotate so that the movable light traps are moved to reset positions; if no microspheres occur in the light traps, moving the movable light traps directly to the reset positions.

The invention belongs to the technical field of organic molecular crystal structure, and specifically relates to a high-precision energy ranking method used in the prediction of organic molecular crystal structure, including determining the quantum mechanical action radius of the central unit cell; in the central unit cell, the density block interaction algorithm is used to carry out Energy calculation; within the range of radius R, the effect of molecules outside the central unit cell on the molecules in the central unit cell can be calculated under the precision of quantum mechanics; under the condition of classical molecular mechanics precision, outside the range of calculation radius R, the periodically extended unit The action energy of the cell on the molecules in the central unit cell; calculate the total energy of the crystal, which includes the energy in the central unit cell and the energy between the central unit cell and the periodically extended unit cell. The invention improves the energy calculation efficiency in the drug molecular crystal, and the precise energy feedback will guide the CSP to find the real low-energy dominant crystal form in the correct direction during the crystal prediction process.

The invention discloses a method for calculating activation energy and a reaction rate constant in arene hydrogenation reaction at different temperatures by a computer. The method comprises the steps of: 1, according to the Visualizer module of MS (Microsoft) software, drawing the molecular formulas of a reactant and a resultant in the arene hydrogenation reaction; 2, according to a Geometry Optimization function in the Forcite module of MS software, carrying out the treatment of molecular mechanical energy minimization; 3, according to the Geometry Optimization function in the DMo13 module of the MS software, carrying out the treatment of quantum mechanical structural optimization, and according to an Energy function in the DMo13 module of the MS software, calculating the reactant energy at different temperatures; 4, according to the Reaction Preview function of the MS software, generating the document of reaction trajectory, and according to a TS Search function in the DMo13 module of the MS software, searching a reaction transition state configuration; 5, according to an Energy function in the DMo13 module of the MS software, calculating the transition state energy at different temperatures; 6, calculating activation energy of arene hydrogenation reaction at different temperatures; and 7, according to the activation energy of arene hydrogenation reaction at different temperatures, calculating the reaction rate constant of arene hydrogenation reaction at corresponding temperatures.

The invention provides a high-throughput single-molecule force spectroscopy method, which includes the following steps: 1) using DNA origami as a base, selecting several modification sites on the DNA origami according to the geometric structure of the DNA origami, and The 5' end of the spotted oligonucleotide chain extends a short target DNA strand, which can be complementary to the DNA short strand immobilized on the AFM probe; Methods The interaction force between two complementary DNA short strands located on DNA origami and AFM probes was measured, and the data of specific force-distance curves were collected. The present invention provides a high-throughput single-molecule force spectrum method with high detection efficiency and improved specificity and accuracy. This simple and efficient high-throughput single-molecule force spectrum method provides quantitative measurement of single-molecule mechanics. An efficient and accurate measurement method.

The invention relates to a method for efficiently optimizing molecular structures in batches. The method mainly solves the problem that in the prior art, a large number of optimized molecular structures cannot be rapidly obtained. According to the method for efficiently optimizing the molecular structures in batches, through VB programming, automatic optimization of large-batch molecular structures is completed through one-time operation of a program; one-time program operation is used instead of multiple times of manual optimization calculation, and molecular structure files are read in batches; molecular single-point energy is automatically calculated; pre-optimization is carried out through a molecular mechanics method, and further optimization is carried out through a quantum mechanicssemi-empirical method to make the energy gradient value of the molecular structure reduced to be below 0.05kcal / (mol.Angstrom), and finally, the stable molecular structure is obtained. Such technicalscheme well solves the problems, and the method can be used for optimizing the molecular structure in batches.

Experimental studies of single molecule mechanics require high force sensitivity and low drift, which can be achieved with optical tweezers through an optical tweezers apparatus for force measurements. A CW infrared laser beam is split by polarization and focused by a high numerical aperture objective to create two traps. The same laser is used to form both traps and to measure the force by back focal plane interferometry. Although the two beams entering the microscope are designed to exhibit orthogonal polarization, interference and a significant parasitic force signal occur. Comparing the experimental results with a ray optics model, the interference patterns are caused by the rotation of polarization on microscope lens surfaces and slides. Two methods for reducing the crosstalk are directed to polarization rectification by passing through the microscope twice and frequency shifting of one of the split laser beams.

Disclosed in the present invention are an affinity ligand polypeptide library of immunoglobulin G constructed based on a protein A affinity model and the use thereof. On the basis of a human IgG-protein A composite structure, a key residue of protein A having a relatively high affinity effect on a human IgG is obtained by parsing, and based on which an affinity polypeptide library of IgG is constructed. Further, a candidate polypeptide is gradually screened using an amino acid positioning method, molecular docking and molecular dynamics simulation means. A polypeptide affinity ligand capable of effectively separating and purifying IgG is determined through an affinity chromatography test method.

The invention relates to a method for testing the temperature characteristics of carbon nanotubes. The method combines quantum mechanics and molecular dynamics, and uses density functional theory to test the conductivity of carbon nanotubes under different temperature conditions from the molecular level to the atomic level. , so as to obtain its temperature characteristics. From the perspective of quantum mechanics, combined with the method of molecular dynamics, the present invention first uses molecular mechanics to simulate the real structure of molecules in different environments, saving time and effort, and then uses quantum mechanics to calculate its temperature and conductivity properties, so that it can be quickly and accurately The method is simple and effective to obtain test results.

The invention provides a design method for cutting and inducing graphene to spontaneously crimp to form a carbon nanocone. The design method comprises the steps: 1) constructing circular graphene sheets in different semidiameters in MaterialsStudios software, 2) cutting out a gap in each circular graphene sheet from a circle center in any semidiameter direction, and 3) carrying out molecular mechanic optimization and dynamic simulation on the cut graphene with a Discover module in the MaterialsStudios software to form a carbon nanocone configuration finally. The invention provides the design method of change of the graphene sheets to a CNC (Computer Numerical Control) structure via cutting by using a computer simulation technology, regulation and control of structural parameters of the graphene sheets such as a cone angle and length can be achieved; and the provision of the method has important guide significance on experimental preparation of the carbon nanocone.