82 results about "Protein Feature" patented technology

The invention discloses a drug target prediction method and device, electronic equipment and a storage medium. The method comprises the following steps: performing dynamic gating fusion on graph structure features and sequence features of a target drug to obtain drug features; performing dynamic feature enhancement on the digitized sequence of the target protein, and further obtaining protein features through context sensing optimization; obtaining a target affinity score of the target drug and the target protein by using a prediction model based on the drug characteristics and the protein characteristics; wherein the prediction model is obtained through feature representation training marked with actual affinity scores on the basis of a neural network. According to the method, the prediction precision of drug target interaction is improved through deep fusion of drug multi-modal features and protein sequence context perception optimization. The method can realize high-precision prediction of the drug target, and can be widely applied to the technical field of drug target prediction.

The invention discloses an lncRNA-protein interaction prediction method based on bidirectional intention, and belongs to the technical field of bioinformatics, and the method comprises the following steps: data acquisition and preprocessing: constructing a data set; performing lncRNA feature extraction through a multilayer convolutional neural network; carrying out protein feature extraction based on an ACmix module; fusion of the lncRNA and protein bimodal features is carried out through a bidirectional intention network; performing lncRNA-protein interaction prediction on the fusion representation by using a three-layer and multi-layer perceptron network, and outputting at an output layer; and meanwhile, designing a loss function to carry out model optimization. The model is more comprehensive and accurate when the dependency relationship between the sequences is captured, so that the reliability and generalization ability of prediction are effectively improved.

The invention provides a drug target prediction method based on cross-modal attention and uncertainty evaluation, and belongs to the technical field of drug target prediction. In order to solve the technical problems that the existing drug target prediction lacks quantitative evaluation on the reliability of a prediction result and a nonlinear interaction relationship between a drug and a target is difficult to establish, the method comprises the following steps: collecting data, and fusing graph structure features and sequence features of extracted drug molecules to obtain a final code of the drug molecules; extracting amino acid sequence characteristics of the target protein, and constructing protein sequence characteristic expression; inputting the drug molecular features and the protein sequence features into a cross-modal attention module, and aligning and fusing the drug features and the protein features by using a bidirectional cross attention mechanism to obtain drug-target combined feature representation; introducing an uncertainty quantification mechanism, and outputting uncertainty estimation of a drug-target interaction prediction label and a prediction result; the method is used for predicting drug target interaction.

The present invention relates to the field of biomedical technology and discloses an artificial intelligence-based anti-tumor drug resistance detection method and system, comprising: collecting genomic data of tumor cells and analyzing genetic changes in tumor cells; extracting tumor molecular markers from tumor cells and constructing a knowledge graph of anti-tumor drug resistance in tumor patients; extracting gene-protein features of tumor cells and identifying the pharmacochemical properties of anti-tumor drugs; fusing gene-protein features and pharmacochemical properties to perform dimensionality reduction processing to construct a drug resistance analysis model for tumor cells; analyzing drug-target interaction relationships in tumor patients and extracting gene-resistance association features of tumor cells to identify the model reliability of the drug resistance analysis model; defining the result interpretation of the drug resistance analysis model, and combining the model reliability and result interpretation to output the anti-tumor drug resistance detection results of tumor patients. The present invention can improve the accuracy of anti-tumor drug resistance detection.

The invention discloses a drug sequence descriptor-based drug and target interaction prediction method, and belongs to the technical field of drug target prediction. According to the method, the descriptors of the smiles sequences of the two drugs are adopted, and after the two descriptors are added, prediction of the model on the result is more accurate due to the fact that the two descriptors contain structural information and chemical information related to tasks; for protein sequences, the characteristics of a large language model ESM-2 and the characteristics of a BERT large language model are added, and the model weights of the ESM-2 model and the BERT model are derived from tens of thousands of protein sequences, so that the representation capability of output vectors is very high; the interaction between protein features and drug features from a source sequence is realized through the designed cross attention layer with the shared weight, the prediction precision of the model is further improved, and experiments show that the model designed by the invention has a better effect on multiple indexes on multiple data sets.

The application relates to the technical field of computer-aided drug design, and provides a molecule generation method, system, medium and equipment for drug discovery, which comprises the following steps: acquiring a SMILES string of a ligand and an amino acid sequence of a target protein, respectively extracting a ligand feature vector and a protein feature vector, splicing and fusing, and then predicting a binding affinity value through a multilayer perception machine; taking the protein feature vector as a condition, generating a new molecular potential representation through a reverse denoising process of a conditional diffusion model; wherein, at each step of the reverse denoising process, a graph-level readout operation is performed on pure noise, an affinity value is predicted through the multilayer perception machine, a gradient of an affinity guidance loss is returned to a noise prediction network, and the new molecule generation is guided to a high affinity area; and the new molecular potential representation is decoded into a SMILES string through a pre-trained molecular language decoder. Novel molecules with high binding potential can be quickly generated.

Embodiments of the present application disclose a drug screening method, device and computer readable storage medium; after obtaining protein information of a target protein and molecular information of a candidate drug molecule, the target protein is a target macromolecule which can be acted on by the drug molecule, then, feature extraction is performed on the protein information and the molecular information respectively to obtain protein features of the target protein and molecular features of the candidate drug molecule, according to the protein information and the molecular information, interaction information of the target protein and the candidate drug molecule under a molecular force field is determined, then, based on the protein features, the molecular features and the interaction information, a binding strength between the target protein and the candidate drug molecule is calculated, and according to the binding strength, a target drug molecule is screened from the candidate drug molecule; the scheme can improve the accuracy of drug screening.

The invention discloses a macromolecular protein cutting method and system based on multi-source protein feature scoring, and a storage medium, and belongs to the field of computational biology and intelligent drug research and development. In order to solve the technical problem that macromolecular protein is difficult to directly input into an existing calculation model, an amino acid position cutting comprehensive score is obtained by obtaining multi-source feature data such as a protein disorder region and structural domain annotation, candidate cutting sites are screened and a final cutting scheme is determined in combination with double constraints of a structural domain hard boundary and fragment length, and the method is suitable for large-scale industrial production. And generating a protein fragment adaptive to downstream calculation. According to the method, the integrity of the protein structural domain is guaranteed, the cut fragment can be directly used as model input such as AlphaFold, the accuracy and stability of structural prediction and molecular docking are improved, the method is suitable for scenes such as virtual screening and computer-aided drug design, and the problem that an existing cutting method is lack of systematic consideration is solved.

This invention discloses a drug target affinity prediction method that integrates PPI quality and uncertainty. The method constructs a drug molecule map and a multimodal protein structure representation, and extracts multi-source features by combining the local PPI sub-map of the target protein. By calculating the protein's low-frequency level, prediction uncertainty, and PPI quality, a PPI quality-aware gating factor is generated to adaptively adjust the PPI information injection intensity, and a residual enhancement strategy is used to preserve the original protein features. Subsequently, the drug representation and the enhanced protein representation are fused using adaptive gating, and the result is input into a prediction network to output the drug-target affinity. This method effectively integrates protein function and interaction information, improves the prediction stability of low-frequency proteins and the model's generalization ability, and provides an accurate and reliable computational tool for drug screening and candidate molecule selection.

The application provides an immunogenic epitope prediction method based on antigen presentation and immunogenicity feature fusion, comprising the following steps: extracting peptide segments and type I human leukocyte antigen protein features from an immunogenic epitope database by using a constructed feature extraction module; inputting the peptide segments and type I human leukocyte antigen protein features into a pre-trained antigen presentation prediction model to obtain an antigen presentation probability based on the antigen presentation prediction model; inputting the peptide segments, type I human leukocyte antigen protein features and antigen presentation probability information into an immunogenicity prediction model to realize fusion of antigen presentation and immunogenicity features, and obtaining an immunogenicity score representing a T cell activation probability of the peptide segments based on the immunogenicity prediction model, so as to realize prediction of the immunogenic epitope. The application improves the prediction accuracy of the immunogenic epitope.

The application discloses a kind of lncRNA-protein interaction prediction methods based on bidirectional intention, belong to bioinformatics technical field, including the following steps: data acquisition and pre-processing, construct dataset;Through multilayer convolutional neural network, lncRNA feature extraction is carried out;Based on ACmix module, protein feature extraction is carried out;Through bidirectional intention network, the fusion of lncRNA and protein double mode features is carried out;LncRNA-protein interaction prediction is carried out to the fusion representation using three-layer multilayer perception machine network, and output is carried out in output layer;While designing loss function carries out model optimization.The model of the application is more comprehensive and accurate when capturing intersequence dependence, thereby effectively improving the reliability and generalization ability of prediction.

The invention belongs to the field of artificial intelligence algorithm application-drug target interaction prediction, and relates to a DTI prediction method based on LLM and RBMO. Firstly, through data collection, integration and redundancy elimination, a batch of drug target sequences with a significant positive and negative sample imbalance problem are obtained as input data; then, a K-BERT model is adopted to extract deep features represented by drug molecules SMILES, and a ProstT5 model is applied to analyze high-dimensional information of a protein sequence; and then, introducing an RBMO and KNN combined feature selection method to intelligently screen protein features, and finally selecting 513 key features with the best biological discrimination ability. And finally, combining a multi-core feature fusion mechanism with an emerging Kolmogorov-Arnold network (KAN) so as to enhance the analysis and characterization capability of the model on complex biomolecular features.

The invention discloses a drug target affinity prediction method, electronic equipment and a computer readable storage medium, the method comprises the following steps: feature extraction is carried out on input small molecule SMILES and protein sequences, and the small molecule adopts 10 molecular fingerprints of RDK, Topological, MACCS, AtomPair, ECFP4, FCFP4, FCFP6, Avalon, Layered and Pattern to construct mixed fingerprint features; compressing the high-dimensional molecular fingerprint features to vector dimensions consistent with protein features through linear mapping to realize feature balance, and splicing to form a fusion feature vector; and performing nonlinear interaction and expression enhancement on the fusion features by adopting a multi-expert hybrid module, and finally outputting an affinity prediction value between the small molecule and the protein through a linear regression layer. Through fusion of multi-source chemical fingerprints and deep protein pre-training representation, higher feature expression ability and stronger model generalization are realized; the complexity of the model is reduced through feature mapping and a lightweight multi-expert hybrid model, so that the model has better stability and expandability.

The invention relates to the technical field of biological information, and discloses a peanut protein interaction prediction method and system based on deep learning, and a medium. The method comprises the following steps: generating a word embedding vector for a peanut protein sequence through k-mers and Word2Vec algorithms, and splicing the word embedding vector with one-hot codes, physicochemical characteristics and PSSM information to obtain a comprehensive characteristic vector; screening key sites according to the PSSM conservative score to construct a feature matrix; a compressed feature vector is obtained through multi-layer neural network dimension reduction compression; after the two protein feature vectors are randomly spliced, the interaction probability is calculated through a full connection layer and a sigmoid function; and obtaining a peanut protein interaction prediction result according to threshold binarization classification. The technical problem that an existing deep learning method cannot effectively fuse multi-dimensional biological characteristic information and cannot accurately predict the peanut protein interaction relationship is solved.

The application discloses a multi-component joint detection method, device and application for synchronous analysis of bone metabolism markers. The multi-component joint detection method comprises the following steps: pretreating a serum sample, and simultaneously extracting small molecule sterols, short peptides and protein characteristic peptide segments; adopting a reverse phase chromatography system to perform chromatographic separation on the extracts, and realizing synchronous elution of lipid-soluble substances and polar substances through a variable gradient elution program; and adopting a segmented multi-reaction monitoring mode to perform mass spectrometry detection, and simultaneously detecting high-abundance indexes and low-abundance indexes in bone metabolism markers in a same sampling period. The application realizes synchronous quantitative detection of five bone metabolism markers, solves technical problems such as fragmentation, large concentration span, incompatible chromatographic behavior and isomer interference in the prior art, and improves detection efficiency by more than 400%, and reduces detection cost by 50%-70%.

The present disclosure relates to an alternative protein material prediction device. The device includes a protein feature extractor configured to composite features of protein as sequence features, structural features, and physicochemical features; a protein graph data generator configured to generate nodes based on the sequence features and physicochemical features of the protein and generate edges between the nodes based on the structural features of the protein, thereby generating protein graph network data, and an alternative material protein predictor configured to generate an alternative protein material prediction model for predicting an alternative protein material by learning the protein graph data that reflects the composite features of the protein.

The present application relates to the field of medical informatics, and provide a paliperidone efficacy prediction method and system based on plasma proteomics, the method comprises the following steps: collecting the basic data of the target patient; selecting the protein features through the basic data to obtain the related proteins corresponding to the paliperidone efficacy; training the neural network based on the related proteins and the baseline data in the basic data to obtain the prediction model; predicting the paliperidone efficacy of the patient to be predicted through the prediction model to obtain the prediction result. The present application can predict the treatment response of schizophrenic patients to paliperidone, and significantly improve the objectivity of paliperidone use.

The invention discloses a synthetic protein design method based on protein feature engineering and a diffusion model, which comprises the following steps: firstly, searching a homologous sequence of a query sequence in a non-redundant NR database by using a P-BLAST tool and taking a target protein sequence as the query sequence; carrying out ProtParam-7 and ProtFactor-5 feature engineering on the screened homologous sequences, and carrying out ProtParam-7 and ProtFactor-5 feature engineering on the screened homologous sequences; taking data represented by the ProtParam-7 and ProtFactor-5 characteristics as original proteins, and inputting the original proteins into the diffusion model; performing multi-dimensional screening on the generated candidate proteins; evaluating the functional activity and the structural stability of the candidate protein by adopting a wet experiment, and taking the protein meeting the condition as a final generation result. According to the method, protein sequence feature extraction and diffusion model generation are combined, and multi-dimensional screening and experimental verification are carried out to ensure that the generated protein is close to the target protein in structure and function.

The invention is suitable for the technical field of deep learning, and provides a nucleic acid aptamer generation and screening method and device, electronic equipment and a program product. The method comprises the following steps: inputting a target protein into a protein structure encoder, and extracting a first protein feature of the target protein; inputting the guiding condition and the guiding intensity coefficient into a condition diffusion model to generate at least one candidate nucleic acid aptamer; inputting each candidate nucleic acid aptamer into a nucleic acid encoder, and extracting a first nucleic acid sequence feature of each candidate nucleic acid aptamer; inputting each first nucleic acid sequence feature and the first protein feature into a semantic space alignment module, and calculating a prediction score of each candidate nucleic acid aptamer; adding each candidate nucleic acid aptamer and the predicted score thereof into a nucleic acid candidate pool; and determining the candidate nucleic acid aptamer with the highest predicted score in the nucleic acid candidate pool as the nucleic acid aptamer with the optimal binding capacity with the target protein. According to the invention, efficient generation and screening of the high-affinity nucleic acid aptamer can be realized.

The present invention discloses a method for predicting drug-target binding affinity based on a graph neural network, belonging to the field of bioinformatics. The method comprises the following steps: S1: sample preprocessing; S2: model construction; S3: model training; and S4: DTA prediction. The method first obtains relevant data from the Davis and KIBA datasets. Through data preprocessing, drug molecular graphs, drug Morgan fingerprints, and protein sequence information are obtained, respectively, and input into a GATv2 network, a multi-layer perceptron network, and a multi-scale convolutional neural network for feature extraction. The Morgan fingerprints and molecular graph features are then spliced ​​together using layer attention to obtain drug features. These features are then spliced ​​with protein features and input into a prediction network for drug-target binding affinity prediction.

The embodiment of the invention discloses a protein generation method and device, electronic equipment and a storage medium, and the method comprises the steps: firstly obtaining protein demand information which comprises attribute information and functional domain information corresponding to protein; and then, performing feature extraction on the attribute information to obtain protein feature data corresponding to the attribute information, and performing feature extraction on the functional domain information to obtain functional domain feature data matched with a functional domain corresponding to the functional domain information, so as to obtain the protein feature data according to the protein feature data and the functional domain feature data. And generating a target protein containing the functional domain corresponding to the functional domain information. According to the technical scheme, the protein with the specific functional domain can be generated, the matching degree between the generated protein and the protein demand information is improved, and the success rate of protein generation is improved.

The present invention relates to the field of neural network technology of artificial intelligence technology. The present invention provides a method, device, equipment and storage medium for predicting drug-target interactions, wherein the method comprises: calling a pre-constructed graph neural network to extract drug features in a molecular graph of a drug, processing the molecular graph according to a restarted random walk algorithm, predicting the similarity of drug features between two adjacent nodes in the molecular graph, obtaining global structural information, inputting the global structural information into a preset deep neural network, obtaining low-dimensional feature information of the drug, acquiring the protein sequence of the target, calling a long short-term memory network to process the protein sequence, obtaining protein features, inputting the low-dimensional feature information and protein features into a preset fully connected layer to predict the results of the interaction between the drug and the target, and extracting the information contained in the drug and protein sequences in a targeted manner, thereby improving the prediction efficiency of the interaction between the drug and the target.

The present invention relates to the field of drug-target affinity prediction, and in particular to a drug-target affinity prediction method based on a multi-scale hybrid attention network. The present invention utilizes a self-attention mechanism to enable protein pocket residues to learn global residue features, thereby achieving learning of global protein features. Furthermore, a cross-modal feature fusion mechanism is utilized to enhance sequence features of protein and drug structural features. While enhancing intra-entity cross-modal feature fusion, the present invention also utilizes a cross-entity interaction module to identify key atoms in drug molecules or key residues in proteins, thereby improving the overall performance of the model. Finally, the present invention further introduces multi-level protein feature extraction to further extract protein features.

The invention relates to the technical field of computer-aided drug design, and provides a molecule generation method and system for drug discovery, a medium and equipment, and the method comprises the steps: obtaining an SMILES character string of a ligand and an amino acid sequence of a target protein, respectively extracting a ligand feature vector and a protein feature vector, and carrying out splicing fusion to obtain a target protein feature vector; predicting a binding affinity value through a multi-layer perceptron; generating a new molecular potential representation through a reverse denoising process of a conditional diffusion model by taking the protein feature vector as a condition; wherein in each step of the reverse denoising process, performing graph-level read-out operation on pure noise, inputting a multi-layer perceptron prediction affinity value, returning the gradient of affinity guide loss to a noise prediction network, and guiding new molecule generation to face a high-affinity region; and decoding the new molecular potential representation into an SMILES character string through a pre-trained molecular language decoder. And a novel molecular structure with high binding potential can be rapidly generated.

The invention provides a system for predicting the applicability of triple negative breast cancer neoadjuvant immunotherapy. Specifically, the system comprises at least one detection unit comprising determining a multi-modal feature of a subject to be detected, the multi-modal feature comprising, or consisting of, a clinical pathological feature, a copy number variation feature, a plasma protein feature, and a somatic mutation feature; the system further comprises at least one data analysis unit and at least one judgment unit. The system is used for predicting new auxiliary immunotherapy of the triple negative breast cancer, and has excellent sensitivity and specificity.

This disclosure provides methods for identifying subjects with cancer who will not respond to or are unlikely to respond to treatment (e.g., immune checkpoint inhibitor monotherapy), wherein the cancer has altered (e.g., increased or decreased) expression levels of a set of biomarkers, and methods for providing additional cancer treatment to the subjects with cancer using said methods.

This invention discloses a multi-target drug design method based on protein sequence and similarity features. A multi-target drug design model is designed, consisting of a target feature embedding module, a target feature encoding module, and a multi-target drug generation module. By independently encoding and similarity encoding the features of multiple targets, and then using the encoded feature latent vectors and similarity feature latent vectors, drug molecules targeting multiple protein targets can be directly generated. Specifically, the target feature embedding module is pre-trained on a large protein dataset based on ProtTrans, demonstrating strong protein feature embedding capabilities; the multi-target drug generation module is trained on a large drug-like dataset, achieving strong drug generation capabilities; subsequently, the entire model is trained on a multi-target drug dataset, achieving excellent multi-target drug design capabilities. The designed drug molecules can bind well to each target protein, achieving the goal of multi-target drug therapy.

The invention provides an enzyme directed evolution method and a related device, and relates to the field of enzyme directed evolution. According to protein feature coding data of the candidate amino acid sequence data, activity prediction is carried out on the mutant candidate amino acid sequence data through a prediction model, better target amino acid sequence data is screened out, and then a target amino acid sequence entity is constructed through automatic experiment operation; according to the method, the catalytic activity of the enzyme is measured to obtain the actual catalytic activity, the actual catalytic activity is verified, the verified actual catalytic activity is used for model optimization operation, and directed evolution of the enzyme is realized in a mode of combining a model and an experiment, so that a'prediction-automatic experiment-data feedback-iterative optimization 'closed-loop system can be constructed. Besides, the prediction model uses self-adaptive sorting loss, so that the prediction model pays more attention to whether the sorting relationship between the predicted values of the samples is consistent with the sorting relationship of the true values, the recognition capability of high-activity amino acid sequence data is improved, and the directed evolution accuracy is improved.

The present invention provides a method and system for predicting protein toxicity based on sequence information. The method comprises obtaining multiple protein sequences from a protein database; performing feature calculation on all protein sequences to obtain protein feature vectors for six categories; concatenating the six feature vectors by column to obtain a first feature vector; performing dimensionality reduction screening on the first feature vector to obtain a second feature vector of the target dimension; using the second feature vector to train a graph attention-based neural network model, and using the trained neural network model as a protein toxicity prediction model; inputting a new protein sequence into the protein toxicity prediction model to obtain a toxicity prediction result output by the protein toxicity prediction model. The present invention is adaptable to different types of protein sequences and accurately predicts protein toxicity by learning common sequence patterns.

This invention relates to the field of biological aging assessment technology, specifically a method for assessing cellular aging based on proteomics data and machine learning. The method includes: constructing a cell type-specific candidate feature set based on single-cell transcriptomics data; obtaining a protein feature matrix based on plasma proteomics data; constructing independent machine learning-based cell type-specific aging prediction regression models for each cell type, using age as the response variable and the protein feature matrix as input; inputting the proteomics data of the sample to be predicted into the corresponding cell type-specific aging prediction model to obtain the predicted lifespan and the lifespan difference characterizing cellular aging for different cell types. This invention achieves quantitative assessment of the aging degree of different cell types in different organs under in vivo conditions by constructing a functional mapping bridge between single-cell transcriptomics and plasma proteomics.