46 results about "Molecular conformation" patented technology

The invention discloses a preparation method and application of a membrane separation material based on external field enhanced water isotope separation. The preparation method comprises the following steps: firstly, pre-enriching a precursor component containing a polymerizable monomer, a cross-linking agent and a photoinitiator in a confinement pore channel of a nano-porous carrier through an impregnation-encapsulation strategy; and then, through in-situ photo-initiation polymerization, a covalent cross-linked functional polymer network is constructed in the pore channel, and stable packaging of the polymer is realized. In the water isotope separation period, external field conditions are regulated and controlled, the molecular conformation of a polymer chain is accurately controlled, and the separation performance is optimized. According to the invention, by virtue of an external field strengthening technology, the intramolecular / intermolecular interaction is destroyed, and the macromolecular chain is converted from contraction to stretching, so that more functional sites are exposed, and the water isotope separation material designed by the invention has a huge practical application prospect.

The invention discloses a molecular multi-mode characterization method based on attention fusion, and the method comprises the following steps: firstly, carrying out the independent feature extraction of the one-dimensional, two-dimensional and three-dimensional modes of a molecule through a molecular sequence encoder, a molecular map encoder and a molecular conformation encoder, and carrying out the feature extraction of the one-dimensional, two-dimensional and three-dimensional features of the molecule; based on natural language text description, multi-level contrast learning is adopted, and gradual alignment of each mode and the text is achieved; secondly, multi-modal consistency constraint is introduced, the characterization distance of the same molecule in different modals is shortened, and semantic consistency is ensured; thirdly, adaptively integrating multi-modal features through a modal attention fusion module to obtain uniform molecular semantic representation, and further performing final alignment with a text embedding space; and finally, completing tasks such as molecule-text bidirectional retrieval and molecule attribute prediction by utilizing fusion representation. According to the method, under the condition that the model does not need to be retrained for different tasks, natural language-driven molecular retrieval, editing and property prediction can be realized, and the method has relatively high robustness, expansibility and universality.

This application provides a method and apparatus for training a molecular multiconformation prediction model. The method includes: acquiring training data, which includes molecular structure representation samples and molecular conformation samples; processing the molecular structure representation samples and molecular conformation samples using the molecular multiconformation prediction model to be trained to obtain a training output; constructing a loss function value based on the training output and the molecular conformation samples; and, if the loss function value or the number of training rounds is within a preset range, using the trained molecular multiconformation prediction model as the molecular multiconformation prediction model. This application can achieve fast and accurate prediction of multiple three-dimensional conformations of molecules without analyzing their potential energy surfaces, reducing the computational resources and time consumed in resolving multiple three-dimensional conformations of molecules.

A method may include identifying an input molecule. A structural representation indicative of a conformation of the input molecule may be generated. In some cases, the structural representation may be a canonical conformation signature or a multimodal representation encoding the three-dimensional structural features of the input molecule. An output molecule may be generated by applying a molecule design computation model to modify the amino acid residue sequence of the input molecule. The modifying of the ammino acid residue sequence may be guided by the structural representations of the input molecule in order to preserve the conformation of the input molecule. In some cases, one or more properties of the output molecule may be determined based on the structural representation of the output molecule. Related systems and computer program products are also provided.

The application discloses a molecular conformation generation method and device based on an evolutionary clustering algorithm. The method optimizes an initial molecular structure input through a local optimization strategy, obtains an optimized initial molecular structure, and generates an initial population based on the optimized initial molecular structure. Clustering analysis is performed through a hierarchical clustering strategy, and a plurality of structure clusters are obtained. Abnormal structure clusters and normal structure clusters are obtained by judging the maximum distance in the clusters. For the abnormal structure clusters, the abnormal structures in the clusters are taken as parents in a set proportion to perform population iteration. For the normal structure clusters, a search strategy is optimized through an adaptive evolution strategy to perform population iteration. An algorithm termination condition is generated based on energy convergence criteria and structure convergence criteria. When the population iteration meets the algorithm termination condition or reaches a maximum iteration number, the iteration is stopped. A molecular conformation meeting energy criteria in the iteration process is output, and a final molecular conformation is obtained. The application can improve the efficiency and intelligent level of structure search.

Systems and methods for property guided molecular optimization using artificial intelligence diffusion models. An equivariant continuous denoising diffusion implicit model autoencoder framework (DDIM-AE) can be trained (510) on a conformational dataset to predict raw data from data corrupted by a time-dependent noise to obtain a trained DDIM-AE that ensures controlled generation of threedimensional (3D) molecules. Linear optimization of semantic embeddings of 3D molecules can be performed (520) with a linear classifier to achieve a target property value from desired properties and obtain an optimized embedding. An optimized 3D molecule that includes molecular conformation with the desired properties while preserving interactions with biochemical molecules can be generated (530) from the optimized embedding with the trained DDIM-AE.

The invention relates to the field of drug delivery, in particular to a prediction method and device for nanoparticle assembly and a program product. Comprising the following steps: acquiring three-dimensional compound molecules of a target compound and a target nanoparticle size; serializing the topological structure of the three-dimensional compound molecule to obtain a topological sequence; obtaining a three-dimensional coordinate of each atom according to the sequence of the atoms in the topological structure to obtain a molecular conformation sequence; discretizing the size of the target nanoparticles to obtain a size sequence; integrating the topological sequence and the size sequence to obtain a first topological sequence, and integrating the molecular conformation sequence and the size sequence to obtain a first conformation sequence; and outputting the first topological sequence and the first conformation sequence to a neural network for feature extraction, and then performing prediction to obtain metal ions, organic compound additives and corresponding three-dimensional conformations of nanoparticles with specified sizes. The method has good application value.

The invention discloses a targeted nutrient source mining method based on beef cattle intestinal type-host gene interaction, particularly relates to the field of biological information data processing, and is used for solving the problems that existing nutrient source development lacks molecular mechanism verification and is poor in targeting. The method comprises the following steps: firstly, dividing nutrition-associated intestinal types based on microbiome and transcriptome data, and constructing a co-expression network to screen host co-expression specific genes driven by the specific intestinal types; then, establishing a flora metabolite ligand set and host protein receptor model, executing molecular conformation search and Gibbs free energy calculation, and screening high-activity targeting effect factors based on physical affinity; and finally, traversal matching and quantitative screening are carried out on the natural raw material liquid chromatography-mass spectrometry data by using the targeted effect factors, and a targeted nutrition source recommendation list aiming at the specific intestine type is generated. According to the method, multi-omics correlation analysis and molecular thermodynamics verification are fused, and an accurate development closed loop from micromechanism analysis to macroscopic raw material matching is constructed.

An artificial intelligence-based compound processing method and apparatus, an electronic device, a computer-readable storage medium, and a computer program product relates to an artificial intelligence technology. The method includes obtaining an active compound for a target protein; performing compound generation processing on an attribute property of the active compound to obtain a first candidate compound; performing molecular docking processing on the active compound and the target protein to obtain molecular docking information respectively corresponding to a plurality of molecular conformations of the active compound; screening the plurality of molecular conformations based on the molecular docking information respectively to identify a second candidate compound corresponding to the active compound; and constructing a compound library for the target protein based on the first candidate compound and the second candidate compound.

The invention relates to acylhydrazone molecules capable of activating solid-state fluorescence or photochromism and preparation and application thereof, in the molecular structure, by changing a substituent R on a-N (R)-group on one side of benzoyl hydrazine, the conformation and accumulation mode of the molecules can be adjusted, so that selective activation of the fluorescence or photochromism property of the acylhydrazone molecules in a solid state is realized. When the substituent R is-H, the molecular conformation is planar, and the intermolecular accumulation is tight. In a solid state, the compound shows an excitation wavelength dependent fluorescence property, and when the wavelength of excitation light is changed, the fluorescence color is switched between blue and green. When the substituent R is-CH3, due to the steric effect of-CH3, the molecular conformation is distorted, and the accumulation among molecules becomes more loose. When ultraviolet light and visible light are alternately used for irradiation in a short time, the color of the powder can be rapidly switched between white and orange. The method provided by the invention is not influenced by R'on a benzene ring, and shows good universality.

The invention relates to the technical field of deep processing of egg products, in particular to egg white peptide / polyphenol / metal ion ternary synergistically assembled composite particles and application of the egg white peptide / polyphenol / metal ion ternary synergistically assembled composite particles in stable emulsions.The egg white peptide / polyphenol / metal ion ternary synergistically assembled composite particles are prepared by pre-assembling metal ions and polyphenol to form a metal-phenolic network and synergistically assembling the metal-phenolic network and egg white peptide through an anti-solvent coprecipitation method. The egg white peptide / polyphenol / metal ion ternary synergistic assembly composite particles are formed. Compared with unassembled egg white peptide, the colloidal property of the composite particle is regulated and controlled, the absolute value of surface charge is reduced, the interface hydrophobicity is enhanced, and the egg white peptide molecule conformation is promoted to be converted into an ordered secondary structure mainly comprising beta-folding. The composite particle can be used as a novel stabilizer for constructing an emulsion, and the obtained emulsion is uniform in droplet size, good in dispersity and still stable under the environmental stress conditions of heating, freezing and thawing, different pH values, salt ion strength and the like. The invention provides a new technical approach for the application of the egg white source active peptide in emulsion and functional food.

This invention discloses a machine learning-enhanced fluorescence detection method for silver nanoclusters containing split nucleic acid aptamers, used for the detection of adenosine triphosphate (ATP) in aquatic products, belonging to the field of analytical chemistry. This detection method uses two split nucleic acid aptamers of ATP as templates to synthesize DNA-AgNCs. In the presence of the target ATP, a conformational change is induced, resulting in a decrease in fluorescence intensity. Quantitative analysis of ATP is achieved by detecting this fluorescence change. To further improve the detection effect, machine learning is introduced to preprocess the fluorescence spectrum. A recursive feature elimination algorithm is used to screen characteristic wavelengths, and a multi-dimensional feature set is constructed using maximum fluorescence intensity, peak area, and full width at half maximum (FWHM). The optimal classification model is obtained through cross-validation optimization. This invention combines aptamer recognition, DNA-AgNCs, and machine learning to construct a detection method where fluorescence dynamically decreases with increasing ATP concentration. It has advantages such as low cost, simple operation, and good biocompatibility, effectively improving detection sensitivity and stability, and has promising application prospects in the qualitative and quantitative analysis of ATP in aquatic products.

The application provides a method, device, equipment and computer readable storage medium for virtually screening coordination inhibitors, which comprises: obtaining a plurality of candidate ligand molecules containing at least one coordination warhead in a coordination warhead set; performing molecular docking on the plurality of candidate ligand molecules and target proteins respectively to obtain a plurality of molecular conformations after docking; screening a first set of molecular conformations according to the distance between the coordination warhead in the plurality of molecular conformations and the coordination center of the target protein; obtaining the first binding free energy of the first set of molecular conformations after docking with the target protein according to a first binding free energy calculation method, and screening a second set of molecular conformations; screening a third set of molecular conformations from the second set of molecular conformations, wherein the target molecular conformations in the third set of molecular conformations satisfy the first preset condition of the second binding free energy and / or the second preset condition of coordination energy; and determining the coordination inhibitor according to the third set of molecular conformations. The application can improve the screening efficiency and success probability of the coordination inhibitor.

This application relates to the field of medicinal chemistry, specifically disclosing an antitumor molecular gel compound and its preparation method. It is prepared from the following raw materials: phthalic anhydride or its substituted derivative, a 2-amino-6-substituted benzothiazole derivative, a condensing agent, an organic base, and a polar aprotic solvent. The preparation method is as follows: S1, dissolving the 2-amino-6-substituted benzothiazole derivative and the organic base in a solvent; S2, dissolving the phthalic anhydride or its substituted derivative in the solvent and adding it dropwise to a first mixture to obtain a second mixture; S3, adding the condensing agent to the second mixture; S4, quenching the reaction solution in ice water and extracting with ethyl acetate; S5, separating and purifying the crude product by column chromatography. The compound of this application can be used to develop novel antitumor drugs that target and degrade tumor-related proteins, possessing advantages such as molecular conformational stability, optimized physicochemical properties, hydrophobicity regulation, and enhanced binding affinity.

This invention discloses a nicotine-capturing smoking cessation drug composition based on molecular configuration matching, belonging to the field of smoking cessation drug technology. The drug consists of three organic functional molecules screened by molecular structure (each molecule has a specific configuration, see Figure 2) that self-assemble in a specific molar ratio under human physiological conditions to form a three-dimensional molecular cage. This molecular cage, through precise adaptation of its internal cavity configuration to the chair conformation of nicotine molecules (the configuration after binding is shown in Figure 3), specifically recognizes and encapsulates nicotine molecules, preventing them from crossing the blood-brain barrier and entering the brain by increasing molecular weight and enhancing polarity. This blocks the nicotine addiction reward pathway at its source, thereby eliminating nicotine addiction and physiological dependence. The drug of this invention only acts in the peripheral circulation, does not enter the central nervous system, does not act on brain nerve receptors, has no psychotropic side effects, and is non-addictive. The molecular cage-nicotine complex can be normally metabolized and completely excreted from the body. This invention, with precise molecular configuration matching as its core innovation, has a novel mechanism, extremely high safety, and gentle withdrawal, effectively reducing relapse rates. It is suitable for various nicotine-dependent populations and has extremely high clinical translational and patent protection value.

The application discloses a cancer targeting drug generation method based on differential geometry and reinforcement learning, belongs to the intelligent control technical field, and accurately describes the geometric characteristics of a molecular surface through differential geometry, generates diversified and chemically reasonable molecular conformations through DDPM, expands a molecular library in combination with a genetic algorithm, and optimizes the binding affinity of a molecule and a mutant target protein through reinforcement learning. The cancer targeting drug generation method based on differential geometry and reinforcement learning provided by the application does not need the complex post-processing of traditional methods, has a simple structure, is high in efficiency, and provides a brand-new technical paradigm for cancer targeting drug design.

The invention discloses a quick verification system and method for docking and RMSD optimization applied to the field of biomedical computational simulation, and the method comprises the steps: constructing a multi-stage screening and error compensation mechanism of a molecular conformation, controlling the computational complexity through employing a discretized grid in an initial sampling stage, compressing a candidate space through employing a quick energy function in a coarse screening stage, and carrying out the quick verification of the RMSD optimization. Gradient-driven local optimization is introduced in the refinement stage to improve the structural precision, a residual error correction module based on a neural network is deployed in the final stage to carry out nonlinear correction on systematic coordinate deviation, a closed-loop optimization process is formed, and on the premise that the process does not depend on quantum mechanical calculation with high calculation cost or long-time molecular dynamics simulation, the precision of the system is greatly improved. The root-mean-square deviation of the docking conformation is stably controlled within 0.5 angstroms, and meanwhile, the single molecule processing time is kept at the order of fifty milliseconds, and the speed is increased by more than 20 times compared with a traditional high-precision docking method.

The application discloses a fluorescent probe molecule luminous intensity quantification method and system, and belongs to the technical field of fluorescent probes. The fluorescent probe molecule luminous intensity quantification method comprises the following steps: building an initial structure of a fluorescent probe molecule and performing molecular dynamics simulation, uniformly extracting a plurality of molecular conformations from a motion trajectory; performing excitation state property calculation on each molecular conformation, extracting an excitation wavelength and an excitation intensity corresponding to a maximum excitation state oscillator strength; performing excitation state geometry optimization on each molecular conformation, extracting an emission wavelength, an emission intensity and an emission energy; calculating a luminous intensity coefficient based on the wavelength parameter, the intensity parameter and the energy parameter; evaluating the luminous performance of the probe molecule according to the luminous intensity coefficient, and screening a probe molecule with the largest luminous intensity coefficient as a target probe. The application can convert a dynamic effective object which is difficult to directly measure into a numerical form which can be measured and calculated, and realizes the standardization, dynamicization and repeatable quantitative characterization of the luminous intensity of the probe molecule.

The application relates to a virtual screening method, device and electronic equipment. The method comprises the following steps: performing molecular docking on ligand molecules in a molecule library and target proteins to obtain at least one molecular conformation after the ligand molecules contact the target proteins; determining a first binding free energy of the molecular conformation after the ligand molecules contact the target proteins by using a preset scoring function, and screening a molecular conformation whose first binding free energy meets a first preset condition; and determining a second binding free energy of the molecular conformation whose first binding free energy meets the first preset condition after the ligand molecules contact the target proteins based on a semi-empirical molecular orbital method, and screening a molecular conformation whose second binding free energy meets a second preset condition. The scheme provided by the application can quickly predict the binding free energy of the molecular conformation, improve the accuracy of the prediction result, and thus improve the success rate of screening active compounds.

An estimation system comprises at least one processor. The at least one processor acquires a target molecule model representing a conformation of a target molecule, generates a molecule-of-interest model representing a conformation of a molecule of interest, the molecule of interest being a molecule capable of binding to the target molecule, calculates energy of interaction between the molecule of interest and the target molecule as intermolecular interaction energy based on a positional relationship between the target molecule model and the molecule-of-interest model, calculates energy of interaction in the molecule of interest as intramolecular interaction energy, and estimates a conformation of the molecule of interest based on the intermolecular interaction energy and the intramolecular interaction energy.

The application relates to the technical field of molecular conformation, in particular to a molecular conformation generation method based on a conditional generative adversarial network and a storage medium. The molecular conformation generation method comprises the following steps: representing a to-be-generated molecule and a molecular motif corresponding to the molecule by using an undirected graph, and inputting the undirected graph into a graph neural network for coding to obtain a to-be-processed molecule graph and a molecular motif graph; inputting the to-be-processed molecule graph and the molecular motif graph into a trained conditional generative adversarial network to determine the distance between atoms in the molecule in the molecule graph; converting the distance between the atoms in the molecule into corresponding molecular three-dimensional coordinates; and obtaining the molecular conformation of the to-be-generated molecule according to the molecular three-dimensional coordinates. The molecular conformation generation method based on the conditional generative adversarial network can quickly and accurately generate the molecular conformation, improves the efficiency of drug molecule docking, and simultaneously reduces the screening time of the drug molecule.

The application belongs to the technical field of flavor enhancement materials, and provides a kind of aroma embedding complex based on pea protein amyloid fiber and its preparation method and application.The aroma embedding complex of the application includes pea protein amyloid fiber (PAF), cellulose nanofiber (CNF) and 2,5-dimethylpyrazine.In the aspect of molecular conformation evolution, the orderly arrangement of cross beta-fold structure induced by CNF promotes the further enrichment of hydrophobic sites, forming a "hydrophobic pocket" with more complete structure and better spatial adaptability.Meanwhile, the ordered conformation enhances the hydrogen bond and hydrophobic interaction between PAF and 2,5-dimethylpyrazine molecules, improving the comprehensive affinity of local binding sites.In the aspect of microstructure regulation, the dense network constructed by CNF and PAF cooperatively forms a limited and continuous embedding space, which more effectively constrains aroma molecules in the hydrophobic pocket, further amplifying the overall aroma binding capacity of the system.

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 invention discloses a molecular conformation generation method based on an interpretable diffusion model, and relates to the field of computer-aided molecular modeling, and the method comprises the following steps: obtaining a molecular graph containing node features, edge features and edge indexes; performing linear transformation on the node features, generating query, key and value, calculating attention weight of each attention head, and merging the attention weight to obtain node update feature representation; after the image Transform is stacked by a plurality of multi-head attention layers, the output of a global diffusion module is obtained; transmitting a neural network message based on a local diffusion graph to obtain an intermediate message of node updating; combining a local diffusion edge condition graph neural network, dynamically adjusting the propagation weight of neighbor information according to edge attributes, and obtaining the final output of a local diffusion module; carrying out weighted average fusion on the output of the two modules, and decoding to obtain atomic coordinates; and obtaining a corresponding thermodynamic diagram through atom and chemical bond attribution. The accuracy of molecular conformation generation can be improved, and the interpretability of the generation process is enhanced.

The present application belongs to the technical field of molecular detection, and particularly relates to a single molecule detection method of anti-aging oligopeptide based on solid-state nanopore technology. The method is as follows: the silicon nitride nanopore chip is pretreated to remove surface contaminants; then, the nanopore is prepared on the silicon nitride film loaded on the chip through a dielectric breakdown method; then, the nanopore chip is assembled with a customized flowcell, and the buffer solution containing oligopeptide is added to the cis side of the flowcell; the oligopeptide is driven to pass through the nanopore by applying a bias voltage, and the electrical signal generated when the oligopeptide passes through the nanopore is collected to realize qualitative and / or quantitative analysis of the anti-wrinkle oligopeptide. The method can efficiently provide information about multiple single molecule conformations and surface properties of the anti-wrinkle oligopeptide molecules, and provides a new scheme for rapid detection of products containing the anti-wrinkle oligopeptide, and has great significance for research and development and market supervision of the products.

The invention provides a temperature-sensitive emulsifier, a preparation method and application thereof, and an HIPE emulsion, the temperature-sensitive emulsifier has an A-b-B structure, a chain segment A is a surfactant chain segment, and a chain segment B is a temperature-sensitive polymer chain segment. According to the preparation method disclosed by the invention, the temperature-sensitive polymer with a definite phase change characteristic is introduced, and the surfactant is linked in a block manner, so that the temperature-sensitive emulsifier with the functions of high-temperature hydrophobic foam stabilization and low-temperature hydrophilic activation can be obtained, and the temperature-sensitive emulsifier can realize intelligent conversion of molecular conformation in a specific temperature interval; in-situ switching of double functions of hydrophobic foam stabilization and hydrophilic wetting can be realized by only introducing one emulsifier, compounding residue conflicts of multiple active agents can be eliminated, the preparation process can be simplified, and the energy consumption can be reduced.

The application provides a hydrogel-based enzyme-linked immunoassay kit and a preparation method and use method thereof, the kit is obtained by pre-immobilization coating a specific antibody or antigen in an ELISA microplate, then encapsulating the enzyme-labeled detection antibody or enzyme-labeled antigen in the hole by using a hydrogel, in addition, the sample diluent contains a component for melting the hydrogel, after diluting the sample by using the sample diluent, the sample is added to the kit, and during the incubation process, the enzyme-labeled detection antibody or enzyme-labeled antigen encapsulated by the hydrogel is rapidly released, and the corresponding ELISA reaction is completed. The advantage of the application is that the operation steps of the ELISA detection experiment can be reduced, the operation time is shortened, and the limitation that the traditional process of ELISA needs to be dried and causes influence on the protein molecular conformation is overcome, so that the sensitivity and precision are improved, the performance is excellent, and the stability is good.

The invention discloses an AI high-flux cardiovascular medicine screening system, and relates to the field of cardiovascular medicine screening. Comprising the following steps: establishing a cardiovascular medicine multi-modal database, integrating compound structure data, biological activity data, genomics data and clinical phenotype data, and performing data cleaning, normalization and feature extraction by adopting a standardized process; the method comprises the following steps: establishing a multi-modal drug characterization learning model based on a deep learning framework, processing molecular two-dimensional structure features by using a graph neural network, processing molecular conformation information by using a three-dimensional convolutional network, processing physical and chemical parameters by using a full-connection network, and carrying out heterogeneous feature fusion and unified vector representation through a cross-modal attention mechanism. According to the method, an intelligent screening system covering the whole drug discovery process is constructed, so that collaborative precise prediction and multi-objective optimization of the activity, toxicity and pharmacokinetic properties of the compounds are realized, and the efficiency and success rate of discovery of the cardiovascular lead compounds are remarkably improved.