9 results about "Molecular mechanics" patented technology

This invention discloses a method for predicting the liquefaction temperature of a gas, comprising: obtaining an initial gas crystal structure; obtaining a stable molecular mechanical environment gas crystal structure based on density functional theory; obtaining a stable force field energy environment gas crystal structure using Compass II force field optimization; calculating the average interaction force and density of each single molecule in the two gas crystal structures respectively; comparing the average interaction force and density of the two gas crystal structures to obtain an initial liquefaction temperature prediction model; continuously adjusting the force field parameters of the initial gas crystal structure in the initial liquefaction temperature prediction model to update the initial liquefaction temperature prediction model to obtain the best-fitting liquefaction temperature prediction model; and incorporating the amorphous unit cells of multiple gas molecules to be tested into the best liquefaction temperature prediction model to obtain liquefaction temperature curves and determine the liquefaction temperature range. The gas liquefaction temperature prediction method disclosed in this invention can accurately predict the liquefaction temperature of a gas.

The application discloses a kind of screening and anti-myeloma application of targeting c-Maf small molecule inhibitor, especially provide the application of sorafenib or glimepiride in preparation anti-myeloma drug.Aspect.The application discloses a kind of method for screening targeting c-Maf small molecule inhibitor, it includes the steps based on molecular virtual screening docking.It is found that potential compound glimepiride and sorafenib can inhibit the activity of c-Maf by the method of the application through virtual screening, molecular dynamics (MD) simulation, molecular mechanics and MM / GBSA free energy calculation and experimental analysis, both can induce the cycle stagnation and cell apoptosis of myeloma cell.The method of the application can screen more targeting c-Maf small molecule inhibitor, it is also helpful to further structure optimization based on sorafenib and glimepiride in the future, and design c-Maf small molecule inhibitor with better activity.

The invention discloses a free energy curve acquisition method and system of drug molecule conformation and electronic equipment, and relates to the technical field of cross of computational chemistry, quantum computation and molecular simulation, and the method comprises the following steps: partitioning a drug molecule composite system into a quantum mechanics QM region and a molecular mechanics MM region; determining conformation coordinates and setting a plurality of sampling windows; constructing a total Hamiltonian for each window, and calculating a final first-order reduced density matrix and a final second-order reduced density matrix; based on the final first-order reduced density matrix and the final second-order reduced density matrix, calculating a conformation coordinate analysis gradient as an average force; and integrating the average forces of all the windows to reconstruct a conformation free energy curve. According to the method, self-consistent coupling is realized through QM / MM partition and quantum evolution, and the calculation precision and stability are improved; analyzing the gradient by using the reduced density matrix to avoid noise; the average force is integrated to reconstruct the free energy curve, the precision is ensured, the cost is reduced, and the method is suitable for complex polarization environments.

The present application relates to a molecular detection method, which uses multi-channel single molecule mechanics technology to simultaneously manipulate multiple molecular probes to detect the analyte; the two ends of the molecular probe are connected to the carrier through the labeled coupling functional groups; the carrier is used to apply pulling force to the molecular probe. The detection process includes binding force and detection force: under the binding force, the molecular probe binds to the analyte; under the detection force, the length difference or length change curve difference of the molecular probe with or without the analyte is used as the signal strength to detect whether the analyte exists, the concentration of the analyte, the binding speed and the binding strength of the analyte to the specific structure. The present application is suitable for detecting the following analytes, such as proteins, drugs, small molecules, DNA, RNA and their complexes.

The present invention provides a molecular force field multi-objective fitting algorithm library and the workflow, including: FFOptlterator as the main module for input and output and force field parameter training iteration; EnergyCalculator module used for MM energy and energy derivatives calculation for the required value of each iteration in the optimization algorithm; the PropertyEstimator module used for the thermodynamic property calculation based on the MD simulation. Wherein, when initializing the FFOptlterator and EnergyCalculator objects, the user specifies the training force field parameters, adjustable parameter ranges, system setting arguments, and MD simulation parameters. The invention is suitable for the related applications of molecular force field training and verification, and implement the framework for different training targets, the prediction of different molecular physical properties, the compatibility and conversion of force field parameters in different formats, integration of multi-objective optimization, result analysis and graphing, etc.

The application provides a DFT calculation model optimization method for vibration-electron interaction in X-type double-spiralene configuration, and belongs to the technical field of quantum chemistry multi-scale calculation; first, experimental data of X-type double-spiralene material is obtained through spectral technology, and microscopic detailed data is obtained through quantum chemistry DFT calculation, so that the energy barrier, vibration spectrum, electron cloud density and molecular orbital energy level data of the X-type double-spiralene material are obtained. For the molecular aggregate state, the periodic DFT and molecular mechanics MM coupling method is used, the active area is described by DFT, and the weak interaction area is processed by MM, and the periodic characteristics of the energy band structure are calculated based on the mixed precision calculation framework. The multi-scale coupled DFT algorithm is used to correlate the vibration-electron interaction at the atomic scale with the energy band structure, non-radiative transition and other mesoscopic characteristics of the molecule, and the macroscopic photoelectric characteristics of the material are output, so that the calculation closed loop from the micro to the macro is completed.

The invention provides a multi-scale simulation prediction method for migration of new pollutants in a porous medium, and belongs to the technical field of computational chemistry and environmental science. The method comprises the following steps: constructing an initial atomic scale model, carrying out classical molecular dynamics pre-equilibrium simulation on the initial atomic scale model to obtain an equilibrium state classical model, obtaining an optimized quantum mechanics / molecular mechanics coupling model through production simulation and geometric optimization, extracting multi-scale parameters through a productive simulation track, and obtaining a quantum mechanics / molecular mechanics coupling model. Comprising quantum scale parameters, molecular scale parameters and macroscale parameters. The method overcomes the limitation that a classical molecular dynamics method cannot describe the quantum effect, and is a multi-scale simulation method which is high in precision, low in cost and capable of revealing and predicting the migration behavior of new pollutants in the porous medium from the mechanism level.

The invention discloses a single molecule force spectrum signal automatic analysis method based on optical tweezers, and aims to solve the problems of low analysis efficiency, high subjectivity and signal loss of a noise reduction algorithm in the prior art. The core of the method is that a simulation signal slice data set is generated through a single molecule stretching model, and a fusion perception adaptive noise reduction model is trained; after overlapping sliding slicing and normalization are carried out on force-distance signals collected by the optical tweezers, the model is input for denoising, and the signals are recombined; finally, folding sites are automatically positioned through secondary difference, worm chain model automatic fitting and parameter automatic calculation are carried out, parameters such as the molecular folding structure size and free energy are obtained, and analysis automation of single-molecule force spectrum signals collected through optical tweezers is achieved. The method breaks through the balance problem of noise reduction and signal fidelity, significantly improves the efficiency, accuracy and stability of single-molecule force spectrum analysis, and is suitable for single-molecule mechanical research in the fields of biophysics and molecular biology.

The application discloses application of glycoside compounds in prevention and treatment of plant pathogenic viruses and belongs to the technical field of pesticide antiviral agents.Taking a tobacco mosaic virus coat protein as an example, small molecules including sugar rings, such as Swertiamarin I (A0) and ZINC85593196 (B0), are screened through virtual screening, molecular dynamics simulation, molecular mechanics and MM / GBSA free energy calculation. Based on this, further optimization is carried out, and six compounds similar to the structure of A0, such as 4-methylumbelliferone-beta-D-xyloside (A1), gardenoside (A2), 4-methylumbelliferone-beta-D-pyranoside (A3), 4-methylumbelliferone-beta-D-pyranoglucoside (A4), catalpol (A5) and esculin (hemihydrate) (A6), are obtained, and in-vivo and in-vitro biological activity evaluation is carried out. The active ingredients screened by the above method have good inhibitory effect on plant viruses.