Homology Modeling Service

The homology modeling method is the most widely used protein prediction method. Homology modeling predicts the three-dimensional structure of target proteins based on template proteins. For proteins without experimental crystal structures, homology modeling is undoubtedly an important and effective auxiliary method. The constructed protein model can also be used for subsequent molecular mechanism exploration. Source modeling is a practical method for predicting structure from sequences. There are two prerequisites for this method: First, there are one or several distinguishable structures in the homologous protein of the target sequence. Second, the homology between the target sequence and the protein is high.

Overall solution

• Select template and alignment sequence: Search for template proteins with known crystal structure from protein database and use BLAST and other tools to align sequences;
• Determine whether there is a template available: template sequence and target sequence similarity> 30 %;
• Build the main chain structure: apply the atomic coordinates of the template structure to the target to generate the basic main chain skeleton and then adjust the main chain atom position to make the bone structure conform to the principle of stereochemistry;
• Build the ring area: One method is to model based on known ring structure. Another method is to predict from scratch based on the principles of quantum chemistry;
• Modeling and optimization of the side chain: use target sequence fragments to search the rotamer database to obtain similar fragments, and then construct the side chain structure of this fragment according to its spatial orientation Finally, the energy is minimized to find the lowest energy point, that is, the stable conformation;
• The overall structure is optimized: there is usually unreasonable contact between atoms in the three-dimensional model obtained through the above process, which needs to be eliminated by methods such as simulated annealing and molecular dynamics.
• Structural 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 verification.

Our homology modeling services

CD ComputaBio provides high-quality homology modeling services. The results can help researchers understand the structural properties of the target protein, analyze its "structure-function" relationship, and can be used for drug screening, discovery of potential therapeutic drugs for a disease, or study the interaction between the target and drug. If you need protein structure modeling service, please feel free to contact us.

Advantages for our homology modeling services:

Homology modeling is a general term for the conversion of primary sequences into 3D structures based on template proteins. It is currently the most effective method for protein three-dimensional structure prediction, and is widely used because of its simplicity, efficiency and high accuracy. According to the theory that the conservativeness of the three-dimensional structure of homologous proteins exceeds the protein sequence, under the premise that the identity of the protein sequence is greater than 30%, proteins with unknown structures can use one or more related structures to construct their three-dimensional structure. We provide a variety of protein structure modeling, but not limited to:

• Fold recognition services
• Antibody modeling services 
• Fusion Protein Modeling Service
• Membrane protein modeling services