Homology Modeling Service

Homology modeling, also known as protein comparative modeling, refers to the construction of an atomic resolution model of the "target" protein based on its "amino acid" sequence and the experimental three-dimensional structure ("template") of the related homologous protein. Homology modeling relies on the identification of a more known protein structure or a structure that may be similar to the query sequence, and the alignment in production. The study of mapping residues in the query sequence to residues in the template sequence shows that the Among homologs, protein structures are more conserved than protein sequences, but sequences with less than 20% sequence identity may have very different structures. Evolutionary related proteins have similar sequences, while naturally occurring homologous proteins have similar protein structures. It has been shown that three-dimensional protein structures are evolutionarily more conservative than expected based solely on sequence conservation. The sequence alignment and template structure are then used to generate a structural model of the target. Because protein structures are more conserved than DNA sequences, a detectable level of sequence similarity usually implies significant structural similarity. The quality of the homology model depends on the quality of the sequence alignment and template structure.

Overall solutions

CD ComputaBio provides high-quality homology modeling services. The results can help researchers understand the structural characteristics of the target protein, analyze its "structure-function" relationship, and can be used for drug screening, discover potential disease treatment drugs or study the interaction between the target and the drug. The homology modeling process can be divided into seven consecutive steps:

• Select template and alignment sequence: search for template proteins with known crystal structures from protein databases and use BLAST and other tools to align the sequences;
• Determine whether there is a template available: the template sequence is similar to the target sequence >30%;
• Construct the main chain structure: apply the atomic coordinates of the template structure to the target, thereby generating the basic main chain skeleton and then adjusting the main chain The position of the chain atoms makes the bone structure conform to the principle of stereochemistry;
• Constructing the ring zone: One method is to model the known ring zone structure. Another method is to predict from the beginning based on the principles of quantum chemistry;
• Modeling and optimization of the side chain: Use the target sequence fragment to search the rotamer database to obtain similar fragments, and then construct the side chain structure of this fragment according to its spatial orientation, and finally minimize the energy to find the lowest point of energy, namely Stable conformation;
• Optimize the overall structure: The three-dimensional model obtained by the above process usually has unreasonable contacts between atoms, which need to be eliminated by methods such as simulated annealing and molecular dynamics;
• Structure evaluation: The most common evaluation standard is RMSD, which represents the root mean square deviation of the corresponding atoms between the target protein and the template protein. It can also be submitted to the SAVES server for inspection.

Services items

CD ComputaBio's homology modeling service can reduce the cost of subsequent experiments. Homology modeling 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.