21 results about "Protein Databases" patented technology

The application belongs to the field of bioengineering. The application provides a molecular modification design method for improving the hydrophobicity of the catalytic center of bacillus subtilis protease, which comprises the following steps: searching for a resolved bacillus subtilis protease crystal structure in a protein database PDB, generating an enzyme-substrate complex by docking a hexapeptide substrate through a Glide mode of software, calculating the polar charge of each amino acid residue of polar atoms N and O and H combined thereof within a 10 angstrom range of the catalytic center amino acid of the bacillus subtilis protease by using a PPC force field, calculating the absolute value sum of the polar charge, selecting a potential mutation site of the bacillus subtilis protease, virtually mutating the potential mutation site into a large steric hindrance nonpolar amino acid, calculating the absolute value sum of the polar charge of polar atoms N, O and H within a 10 angstrom range of the catalytic center amino acid of the single-point mutant by using the PPC force field, selecting a virtual bacillus subtilis protease single-point mutant, expressing the mutant and iteratively mutating, re-expressing, obtaining a modified bacillus subtilis protease mutant, and verifying the hydrophobicity. The molecular modification design method can quickly and effectively reduce water molecules in the catalytic center of the bacillus subtilis protease and improve the hydrophobicity thereof. It has been verified that the enzyme modification method is effective and reliable.

The invention discloses an oligomeric protein de novo design method and system, terminal equipment and a computer readable storage medium. The method comprises the steps that functional characteristics of target protein are acquired, and a first design rule is determined based on the functional characteristics; based on the first design rule, extracting a first protein sequence and a second protein sequence from a natural protein database, and determining a second design rule; generating a candidate mutation sequence library according to the first design rule and the second design rule; performing structure prediction and stability calculation on the sequences in the candidate mutation sequence library, and screening out optimized sequences meeting preset requirements; performing functional characteristic simulation verification on the optimized sequence, and if the verification is passed, outputting a final target protein sequence; otherwise, the verification result is fed back to the protein sequence optimization model for iterative optimization design. The problem that the efficiency is low when the oligomeric protein is designed is solved, and the effect of efficiently designing the oligomeric protein from the beginning is achieved.

The invention discloses a preparation method of polypeptide with antioxidant activity, and relates to the technical field of biology. The preparation method comprises the step of preparing polypeptide with an amino acid sequence shown as SEQ ID NO.3 through a solid-phase synthesis method. According to the invention, a plurality of antioxidant active peptides are obtained by using separation and purification and mass spectrum identification technologies and by means of a saury protein database; multiple rounds of screening are carried out by utilizing the DPPH free radical scavenging rate, reducing power, water solubility, biotoxicity and other properties of the active peptide; the interaction between the antioxidant active peptide and the receptor MPO is explored by combining molecular docking, and the in-vitro antioxidant activity of the polypeptide is verified through solid-phase synthesis and cell experiments. Results show that the active peptide obtained through screening has in-vitro antioxidant activity, has good water solubility and is free of biotoxicity.

This invention proposes a method for screening bisphenol A-specific peptides using molecular simulation, belonging to the field of food safety technology. The method includes the following steps: 1) Through protein stacking and molecular docking, the molecular structure and interactions of bisphenol A-protein cocrystal compounds in a protein structure database are comprehensively analyzed to obtain the receptor protein and the original parent chain; 2) Based on the original parent chain obtained in step 1), the parent peptide is obtained by truncation of the parent peptide segment by analyzing the main active amino acids in the molecular docking results; 3) By performing virtual amino acid mutations on the parent peptide obtained in step 2), a peptide library specifically binding to bisphenol A is constructed, and molecular dynamics is used for preliminary screening of the peptides; 4) The peptide chains screened in step 3) are used as specific recognition elements, and peptides labeled with fluorescein isothiocyanate are used to form specific recognition probes. The specific recognition probes are mixed with bisphenol A, and the peptide sequences with the strongest specific binding ability to bisphenol A are screened based on the different fluorescence differences. This invention is mainly applied to the screening of specific recognition elements for toxic and harmful small molecules, active ingredients, and functional factors. This method avoids the complex preparation steps of antibodies and the cumbersome screening process of aptamers, achieving high-throughput design of specific recognition elements.

According to the cyclopeptide capable of specifically recognizing sucralose and the computer-aided optimization design method thereof, through computer simulation, molecular docking, molecular dynamics, deep learning and other technologies, the combination free energy of molecular docking score and molecular dynamics simulation is used as a judgment basis, and the cyclic peptide capable of specifically recognizing sucralose is obtained without a wet test. And the cyclopeptide with high affinity to target small molecules such as sucralose can be rapidly and efficiently designed. Comprising the following steps: extracting a high-quality protein structure from a protein database, splitting the high-quality protein structure into oligopeptide fragments and carrying out geometric fingerprint calculation; through molecular docking with a target small molecule, an optimal peptide fragment is selected and combined for recombination, and the space structure is optimized; and reconstructing a cyclic peptide sequence through information of the affinity layer, the adjacent layer and the shell layer obtained through calculation to obtain the high-affinity cyclic peptide for targeted recognition of the target small molecules. The design cost is greatly reduced, the design success efficiency is improved, and the method has a wide prospect when being used for identifying and detecting sucralose in small molecules such as environmental sewage.

The invention discloses a method for exploring the influence of electromagnetic waves on a protein structure directly based on molecular dynamics simulation. The method comprises the following steps: acquiring target protein from a protein database; constructing a simulation system; adding a protein force field and a water molecule model; solvent molecules and ions are added to neutralize system charges, and energy minimization treatment is carried out; pre-balancing is carried out under the NVT ensemble and the NPT ensemble; performing molecular dynamics simulation on the simulation system, and storing an atomic coordinate trajectory; and performing post-processing on the track file, extracting distance time sequence data between atoms or residues, screening out atom pairs or residue pairs meeting conditions, performing Fourier transform analysis, and judging whether the possibility of resonance with the electromagnetic wave with the specific frequency exists or not. According to the method, the interaction between the protein and the electromagnetic field can be revealed under the atomic resolution without consumption of experimental materials, and an efficient and reliable molecular-level theoretical basis is provided for evaluating the biological effect of environmental electromagnetic radiation.

This invention relates to a peptide sequence generation model and method utilizing intermediate sequence semantic masking (MSA) and diffusion masking mechanisms, specifically a peptide sequence AI model training method incorporating evolutionary information. It innovatively introduces intermediate sequences to address the problem that peptide sequences are too short to directly extract evolutionary information. First, an MSA is constructed for the peptide dataset. For sequences where an effective MSA cannot be constructed, their sequences are compared with a protein database to select intermediate sequences with high homology and appropriate length. Then, MSA data of these intermediate sequences is constructed to guide the AI ​​model in capturing evolutionary features. Model training employs a diffusion language masking mechanism and an MSA Transformer. All regions are randomly masked in the peptide MSA, and peptide mapping regions are masked in the intermediate MSA, enabling embedding modeling and generation of peptides. This method can capture sparse peptide evolutionary information, achieving semantic modeling and efficient generation of peptides, and is applicable to peptide sequence optimization and synthesis in fields such as drug design and protein engineering.

The invention discloses a protein design method and device based on symmetric self-game online reinforcement learning in the technical field of bioinformatics and artificial intelligence. The protein design method based on symmetric self-game online reinforcement learning comprises the following steps: inputting main chain structure information of a target protein, constructing a training set based on a protein structure database, and representing a protein structure as graph data; constructing an isotropic graph neural network EGNN as an infrastructure of a sequence generator, and initializing a first strategy model, a second strategy model and a reference model; and symmetric self-game online training is carried out. According to the protein design method based on symmetric self-game online reinforcement learning, the limitation of existing static supervised learning and single-agent reinforcement learning is overcome, and collaborative optimization and sustainable evolution of a protein sequence under multi-objective constraint are realized.

A method of generating a microbial protein database is disclosed. The method includes: (a) aligning genomic sequences of metagenomic data to reference genomes to obtain a database of microbial species that are potentially present in the at least one microbiome sample, and their relative abundance; (b) refining the database; (c) obtaining protein sequences of said microbes of the refined database and align to the metagenomic data; and (d) selecting those proteins having a % sequence alignment coverage greater than a second predetermined % to obtain a microbial protein database.

The present application relates to the technical field of bioinformatics, and particularly relates to a construction method of a dehalogenating microorganism functional genome database and an analysis method of dehalogenating microorganisms. The construction method comprises the following steps: obtaining dehalogenation-related genes; obtaining seed sequences and homologous sequences of a family to which the dehalogenation-related genes belong based on a Uniprot protein database to obtain a core database; comparing the core database with a homologous protein database, merging sequences of dehalogenation functional gene families obtained through comparison with the core database to obtain a preliminary database; and comparing the preliminary database to a Refseq database of microorganisms in NCBI, and obtaining a complete database through classification, merging of homologous sequences and de-redundancy. The present application constructs an accurate dehalogenation functional gene database based on analysis and search results of multiple databases, which can be used to conveniently and accurately analyze dehalogenating microorganism functional communities in the environment, and has important application value.

The application discloses a sea cucumber-derived active peptide with immunocompetence and a preparation method and application thereof, and belongs to the technical field of biology. An amino acid sequence of the sea cucumber-derived active peptide is shown as SEQ ID NO. 1. The amino acid sequence of the sea cucumber-derived active peptide is obtained by means of a sea cucumber protein database with the aid of separation and purification technology and mass spectrometry identification technology; the interaction between the immunocompetent peptide and a membrane recognition receptor (TLR-2) is explored through multiple rounds of screening and molecular docking technology; and the in-vitro immunocompetence of the polypeptide is verified through solid-phase synthesis and a RAW264.7 cell model. The results show that the novel immunocompetent peptide screened in the application has in-vitro immunocompetence, no biological toxicity, can activate the immune response of macrophages in the body, but will not excessively activate, so that the body is in a healthy and stable state, and the novel immunocompetent peptide has important significance for deep processing of marine protein resources.

The application discloses application of protein Fobut in regulation of pathogenicity of banana fusarium wilt fungus. The application obtains a deletion mutant and a back-supplementation mutant of Fobut by constructing a knock-out plasmid and a back-supplementation plasmid of a gene (Fobut) coding protein Fobut of banana fusarium wilt fungus and transforming corresponding protoplasts respectively. It is found through observation of the phenotype of the deletion mutant and the back-supplementation mutant and pathogenicity analysis that the knock-out gene Fobut can obviously reduce the pathogenicity of banana fusarium wilt fungus, and the pathogenicity is restored after back-supplementation, which indicates that the protein Fobut is related to the pathogenicity of banana fusarium wilt fungus and can be used as a target for prevention and treatment of banana fusarium wilt. The application enriches a protein database related to the pathogenicity of banana fusarium wilt fungus and is beneficial to prevention and treatment of banana fusarium wilt.

The invention discloses a toxoplasma gondii CTL epitope peptide identification method and application. The toxoplasma gondii CTL epitope peptide identification method comprises the following steps: constructing a toxoplasma gondii infection model of an HLA-A * 0201 transgenic mouse; capturing a natural peptide fragment combined with the HLA-A * 0201 molecule from the spleen lymphocyte surface of the infected model mouse through a weak acid elution method; analyzing the captured peptide fragment by adopting a liquid chromatography-tandem mass spectrometry technology, and screening a toxoplasma gondii-sourced specific peptide fragment based on a toxoplasma gondii protein database; through an in-vitro protein renaturation experiment, the binding capacity of the screened candidate peptide fragment and the HLA-A * 0201 molecule is verified; a TAP defect type T2 lymphoblastic cell model is adopted, and the binding stability of the candidate peptide fragment and the HLA-A * 0201 molecule is verified through a fluorescence index. According to the method, through a progressive screening strategy that after natural peptide group screening, a NetMHCpan-4.1 algorithm is adopted for filtering and eliminating host homology, in-vitro pMHC-I renaturation verification and T2 cell binding stability detection are carried out, the clinical transformation value of epitope screening is remarkably improved, and high-confidence candidate molecules are provided for toxoplasma gondii multi-epitope vaccine design.

The application relates to a protein function domain reprogramming method and device based on a TEE server cluster. The method comprises the following steps: receiving protein data to be reprogrammed containing a known function domain sent by a client; performing similar domain retrieval on the known function domain based on a TED database to obtain a target function domain similar in structure; obtaining target replacement protein data corresponding to the target function domain from a protein database; performing protein data correlation comparison and function domain boundary adjustment, completing function domain replacement processing according to an adjustment result, generating reprogrammed protein data and returning the reprogrammed protein data to the client. By adopting the TEE hardware-level security feature and a multi-algorithm collaborative mechanism, the method realizes data security and operation credibility of the whole process of protein function domain reprogramming, and effectively improves the accuracy and reliability of protein function domain replacement.

The invention discloses a preparation method of an active peptide with an antioxidant function, and relates to the technical field of biology. The preparation method comprises the following steps: preparing polypeptide with an amino acid sequence as shown in SEQ ID NO.2 through a solid-phase synthesis method; the polypeptide is the active peptide with the antioxidant function. According to the invention, a plurality of antioxidant active peptides are obtained by using separation and purification and mass spectrum identification technologies and by means of a saury protein database; multiple rounds of screening are carried out by utilizing the DPPH free radical scavenging rate, reducing power, water solubility, biotoxicity and other properties of the active peptide; the interaction between the antioxidant active peptide and the receptor MPO is explored by combining molecular docking, and the in-vitro antioxidant activity of the polypeptide is verified through solid-phase synthesis and cell experiments. Results show that the active peptide obtained through screening has in-vitro antioxidant activity, has good water solubility and is free of biotoxicity.

The application discloses active peptides from coilia nasus with antioxidant activity, and a preparation method and application thereof, and relates to the technical field of biology.The amino acid sequence of the active peptides from coilia nasus is shown in SEQ ID NO.1, SEQ ID NO.2 or SEQ ID NO.3.Through the separation and purification and mass spectrometry identification technology, and with the help of coilia nasus protein database, a plurality of antioxidant active peptides are obtained; the DPPH free radical scavenging rate, reducing power, water solubility, biological toxicity and other properties of the active peptides are used for multi-round screening; the interaction between the antioxidant active peptides and the receptor MPO is explored by molecular docking, and the in-vitro antioxidant activity of the polypeptides is verified through solid-phase synthesis and cell experiments.The results show that the three active peptides screened in the application all have in-vitro antioxidant activity, good water solubility and no biological toxicity.

A method and apparatus for predicting and analyzing RNA-binding residues are disclosed. The method constructs a GDRBind model using PyTorch and the DGL framework; inputs a protein sequence of a predetermined length into the GDRBind model and obtains the protein structure data of the protein sequence; generates a multiple sequence alignment (MSA) file using the protein sequence search software HHblits; collects several RNA-binding protein sequences from the UniProtKB protein database, performs clustering processing to obtain a pre-training dataset, and uses it to train a general protein language model to obtain an ESM-RBP representation model; obtains a first embedding matrix and a second embedding matrix through processing, and concatenates them to obtain a residue node feature representation matrix; calculates the edge features of all residue pairs in the protein sequence to obtain an edge set; and predicts the RNA-binding residues of the protein sequence using an equivariant graph neural network (EGNN) prediction model, outputting the predicted results. This invention can solve problems such as insufficient domain feature mining, low segmentation accuracy, and lack of interpretability.

The invention discloses a method for screening potential alkali-resistant laccase based on molecular dynamics simulation of randomly selected candidate sequences. The method comprises the following steps: acquiring a laccase sequence from a protein database and carrying out redundancy elimination treatment; constructing a phylogenetic tree and randomly selecting candidate sequences from different evolutionary branches; constructing a three-dimensional structure model by using a structure prediction tool; calculating protonation states of protein residues under different pH conditions; evaluating the structural stability of the candidate enzyme under an alkaline condition by adopting molecular dynamics simulation; and screening potential alkali-resistant laccase based on the main chain RMSD and the fluctuation trend thereof. According to the method, an evolutionary diversity sampling strategy is combined with molecular dynamics stability evaluation, so that the alkali-resistant laccase is efficiently screened from a large-scale database, the experimental verification number is remarkably reduced, the screening cost is reduced, and the alkali-resistant laccase mining efficiency is improved.

The invention discloses a halohydrin dehalogenase directional modification method for synthesis of an atorvastatin intermediate, and belongs to the technical field of enzyme directional modification, and the method comprises the following steps: downloading an amino acid sequence of H halohydrin dehalogenase from an NCBI (National Center of Biotechnology Information) protein database, carrying out multi-sequence alignment by using CLUSTALW software, carrying out molecular dynamics simulation, then carrying out PEGylation modification, and carrying out enzyme directional modification. The directionally modified halohydrin dehalogenase is prepared. According to the immobilization method combining the directionally modified halohydrin dehalogenase and the functionalized magnetic porous carrier, the intrinsic activity and stability of the enzyme are improved through directional modification, and the functionalized carrier provides a suitable microenvironment for the enzyme and realizes firm immobilization; the invention not only solves the technical problems of large activity loss, poor stability and the like in the traditional enzyme immobilization process, but also provides an efficient, stable and reusable biocatalyst for industrial application.

The present disclosure proposes a protein language model processing device that generates a chimeric protein language model on the basis of an existing protein language model in order to efficiently and highly accurately achieve the fine tuning of a protein language model. The protein language model processing device executes: processing for referring to a given natural protein database and generating, with respect to known sequence data representing known chimeric proteins, an extended sequence data group which represents a plurality of closely-related proteins that share homology equal to or higher than a predetermined threshold value with each other; and processing for generating a chimeric protein language model by re-training an existing protein language model by using the extended sequence data group as training data (see FIG. 1).

This invention relates to the field of protein processing technology, and more particularly to a protein processing method, apparatus, storage medium, and computer program product. The method includes: acquiring a protein to be processed; generating at least one self-generated protein corresponding to the protein to be processed, wherein the protein to be processed and the self-generated protein are homologous proteins; storing at least one self-generated protein in a protein database, and performing structure prediction on the protein to be processed based on the protein to be processed and / or the self-generated protein in the protein database. This invention addresses the deficiency in existing technologies where the number of homologous proteins is small, leading to inaccurate structural prediction results for structural proteins, and improves the performance of protein structure prediction.