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39 results about "Docking (molecular)" patented technology

In the field of molecular modeling, docking is a method which predicts the preferred orientation of one molecule to a second when bound to each other to form a stable complex. Knowledge of the preferred orientation in turn may be used to predict the strength of association or binding affinity between two molecules using, for example, scoring functions.

Drug-protein interaction prediction model based on convolutional neural network

The invention provides a drug-protein interaction prediction model based on a convolutional neural network, and the construction method of the prediction model comprises the following steps: 1, constructing a bounding box descriptor for a binding site of a target protein, and extracting the spatial structure characteristics of the multi-channel binding site by using a three-layer 3D convolutional neural network; 2, based on the amino acid sequence of the target protein, extracting amino acid composition characteristics of the protein by using a three-layer 1D convolutional neural network; 3, constructing a molecular map for to-be-screened drug molecules, and extracting drug molecule features by using a three-layer map convolutional neural network; and 4, combining all the obtained features to obtain an overall feature, and inputting the overall feature into the two-layer full-connection network to predict drug-protein interaction, so that the method not only considers local features of binding sites closely related to the docking process, but also considers global features of protein, and the characteristics are used for predicting the compound-protein interaction.
Owner:CHINA UNIV OF PETROLEUM (EAST CHINA)

Method for screening pharmaceutically active compounds from traditional Chinese medicines and acting agent

The invention provides a method for screening pharmaceutically active compounds from traditional Chinese medicines and an acting agent. The method comprises the following steps: determining a key signal pathway related to diseases, enabling different traditional Chinese medicine extracts to act on cell lines related to the diseases, and quantitatively analyzing the change condition of a transcription spectrum in cells based on a characteristic gene expression profile, so as to determine the adjusting effect of the different traditional Chinese medicine extracts on the key signal pathway, and selecting traditional Chinese medicines which have effects on the key signal pathway related to the diseases; collecting component compounds of the traditional Chinese medicines from different traditional Chinese medicine databases, and screening potential active compounds from the component compounds according to oral bioavailability and medicine similarity; screening a medicine target which can be used as a medicine effect in the key signal pathway; and further screening the potential active compounds by utilizing the medicine target to obtain the pharmaceutically active compounds. The methodprovided by the invention is a method for screening medicines or small molecular compounds on a large scale on a transcription level by combining a high-throughput medicine screening platform and a second-generation sequencing technology with molecular docking and molecular dynamics simulation, is high in screening efficiency, and provides a new idea for medicine screening.
Owner:CHENGDU UNIV OF TRADITIONAL CHINESE MEDICINE

Method for predicting ligand-protein interaction based on quantum calculation

ActiveCN114446383AAvoid difficultiesOvercoming the inability to train for large problemsQuantum computersMolecular designProtein moleculesBinding site
The invention discloses a ligand-protein interaction prediction method based on quantum computing, and belongs to the field of quantum computing and computational biology, and the ligand-protein interaction prediction method comprises the following steps: obtaining a 3D structure of a ligand drug molecule and a protein molecule; predicting the 3D structure of the protein molecule by using a quantum hidden Markov model to obtain a binding site possibly existing on the protein molecule; docking ligand drug molecules with binding sites, and extracting characteristics affecting ligand-protein docking by using a quantum convolutional neural network; the docking process is scored according to the characteristics affecting ligand-protein docking, and the ligand-protein interaction effect is obtained through prediction. Related information of molecular docking is described based on the quantum convolutional neural network, the quantum hidden Markov model is used for predicting binding sites possibly existing on receptor protein, synchronous prediction of molecular docking and protein structures is achieved, meanwhile, quantum calculation is combined with the field of biological medicine, and the difficulty of protein 3D structure prediction is solved.
Owner:UNIV OF ELECTRONICS SCI & TECH OF CHINA

Ribosome inactivated protein attenuated modification method for blocking receptor binding

The invention belongs to the technical field of bioengineering, and particularly discloses a ribosome inactivated protein attenuated transformation method for blocking receptor binding, which comprises the following steps of: A, predicting a binding site, namely predicting a part where ribosome inactivated protein is bound with a receptor and the binding site by using molecular docking software; b, performing mutation transformation on the amino acid residues of the binding sites according to the prediction result in the step A; c, performing codon optimization according to the mutant gene obtained in the step B; d, synthesizing the whole gene of the target mutant optimized in the step C, and constructing an expression vector; and E, detection: detecting the target mutant gene protein constructed in the step D, detecting whether the target mutant gene protein enters cells or not through a toxicity test and a fluorescence test, and detecting whether the target mutant gene protein is expressed or not. The structural modification mode of the mutation binding site amino acid residues created by the scheme can significantly block alpha-MMC from entering cells and causing cytotoxicity thereof, thereby achieving a significant attenuation effect.
Owner:成都富岱生物医药有限公司

A high-performance computing platform-based computer-aided screening method for nucleic acid aptamers and nucleic acid aptamers

The invention provides a nucleic acid adapter computer-aided screening method based on a high-performance calculating platform, wherein the method relates to the field of molecular biology detecting technology. According to a matching principle, whether a protein structure which matches a target protein exists in a database system which is integrated in a screening platform is determined through searching; if yes, the protein structure is used as an acceptor template; and otherwise, homologous construction is performed. A primary selected nucleic acid adaptor is obtained through modular dynamics simulation and molecular docking screening as a nucleic acid adaptor candidate. The method and the nucleic acid adapter have advantages of high efficiency, high speed and high accuracy. The screening method can be combined with wet-method experiments, thereby reducing the number of the wet-method experiments, saving experiment cost and improving screening success rate. Through computer-aided simulation analysis, information such as chemical reaction mechanism between the protein and nucleic acid molecule in an adaption process is obtained. Furthermore the data are displayed on a terminal. Furthermore a data support is supplied at an aspect of disclosing a possible interaction mechanism between a corresponding biomaterial and the nucleic acid molecule. Therefore the method and the nucleic acid adapter have an important researching meaning and high use value.
Owner:BEIJING COMPUTING CENT +1

Computer-aided screening method for small molecule target nucleic acid aptamers based on high-performance computing platform and small molecule target nucleic acid aptamers

The invention provides a computer-aided screening method for small molecule target nucleic acid aptamers based on a high-performance computing platform, and relates to the technical field of molecular biology. Firstly, analyze the structure of the small molecule target, and then screen in the small molecule compound library. If the matching principle is met, it will be used as the target small molecule target for molecular docking with nucleic acid molecules. If the matching principle is not met, the molecular structure can be constructed. , the small molecule target after molecular structure construction is used as the target small molecule target, and molecular docking is carried out with the nucleic acid molecule. If the docking is successful, the nucleic acid molecule is the primary nucleic acid aptamer, which solves the binding site between the small molecule target and the nucleic acid molecule Small molecular weight, weak affinity, difficulty in grasping nucleic acid molecules, many consumables, small differences in size, mass, and charge properties between the complex formed by the small molecule target and the nucleic acid itself, and the difficulty in separating the two.
Owner:BEIJING COMPUTING CENT

Computer screening method for small molecular covalent inhibitors and application of method to screening of S-adenosylmethionine decarboxylase covalent inhibitors

The invention belongs to the field of biomedicine and particularly relates to a computer screening method for small molecular covalent inhibitors and an application of the method to the screening of S-adenosylmethionine decarboxylase covalent inhibitors. According to the method, in computer-aided screening and design processes of covalent inhibitors, steric hindrance of a protein receptor is reduced or eliminated first and then the protein receptor is used for screening, design and modification of the covalent inhibitors or covalent binding molecules. According to the application of the method to the screening of the S-adenosylmethionine decarboxylase covalent inhibitors, pyruvoyl 68 residues in an S-adenosylmethionine decarboxylase crystal structure are removed and optimization is performed in Rosetta software to obtain an optimized protein crystal structure; docking calculation is performed on small molecules to obtain docking calculation results; and the calculation results are screened to obtain the small molecular covalent inhibitors. According to the method and the application thereof, the perfect docking calculation method for numerous non-covalent inhibitors can be widely used, so that the screening, optimization and discovery of the covalent inhibitors can be greatly accelerated.
Owner:CHINA THREE GORGES UNIV
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