Protein homology detection and sequence alignment are the basis of protein structure prediction, function prediction and evolution. The homology modeling method is the only reliable method to predict the structure of a protein quickly and accurately. In terms of predicting the three-dimensional structure of a protein, it is more than ten times faster than the number and speed that the current experimental methods can achieve. It has the highest accuracy and the most developed. The advantages of maturity, so, for general drug design, the method of homology modeling is mainly used. Through homology modeling, it is easy to build a structural model of an unknown protein.
Every step of homology modeling must be checked for plausibility. Therefore, errors may be accidentally introduced and spread, so model validation and protein evaluation are necessary. The protein model can be evaluated as a whole or in a single area. Initially, the folding of the model can be evaluated by the similarity with the template sequence, or the Ramachandran graph can be used to evaluate the quality of the model.MedAI can use Ramachandran diagrams to provide modeling services. This method is a visualization method used to determine whether the dihedral angles ψ and φ of amino acid residues in the protein structure are within a reasonable range. It can also reflect whether the conformation of the protein is reasonable.
Sequence alignment and alignment are the key steps of homology modeling. It can determine the conserved regions of the sequence by aligning and positioning the sequence of the target protein and the template protein. Sequence alignment is achieved through a series of scoring matrices. Commonly used scoring matrices include identity matrix, codon substitution matrix, mutation matrix, and hydrobocity matrix. In the alignment process, the alignment program regards one sequence as a row and the other sequence as a column, and then constructs the several matrices mentioned above. By comparing each residue unit in the matrix, the arrangement with the highest score is obtained. Commonly used sequence alignment programs are EMBL-EBL. This program can be run only by submitting the template sequence and target sequence online.
|Project name||Homology Detection and Structure Alignment Service|
|Our services||MedAI provides you with Ramachandran map services. The Ramachandran diagram shows the phi and psi of all residues in the protein structure. Glycine and original amino acids are usually removed and processed separately. We can generate Laplacian diagrams of individual amino acids or protein chains. We can also draw the points of the forbidden area in the Laplacian diagram of multiple protein chains: the forbidden area can be understood as a high-energy area, and only an infinite height of energy will cause complete disapproval.|
|Cycle||Depends on the time you need to simulate and the time required for the system to reach equilibrium.|
|Product delivery mode||The simulation results provide you with the raw data and analysis results of molecular dynamics.|
MedAI's homology detection and structure alignment service can reduce the cost of subsequent experiments. Homology detection and structure alignment service is a personalized and customized innovative scientific research service. Before determining the corresponding analysis plan and price, each project needs to be evaluated. If you want to know more about service prices or technical details, please feel free to contact us. If you want to know more about service prices or technical details, please feel free to contact us.
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