Restriction enzymes (REases) are commercial reagents commonly used in recombinant DNA technology. They are attractive models for studying protein-DNA interactions and are important targets for protein engineering. However, some restriction enzymes currently have no crystal structure and require homology modeling. Creative Enzymes provides you with a variety of restriction enzyme homology model generation service to meet your scientific research needs.

Sepcific Restriction Enzyme Homology Model Generation Approaches We Offer

Creative Enzymes offer a one-stop restraint enzyme restriction enzyme homology model generation service that can meet your research needs for restriction enzyme research. Our modeling service is as follows:

• Selection of templates and sequence alignment

We searched the database for templates with known restriction enzyme crystal structures and performed sequence comparisons using tools such as BLAST.

• Determine if the template

The similarity between the template sequence and the target sequence is greater than 30%.

• Main chain structure construction

The atomic coordinates of the template structure are applied to the target to generate the basic backbone of the backbone, and then the atomic positions of the backbone are adjusted to make the backbone structure conform to the principles of stereochemistry.

• Ring region construction

One approach is to model the ring structure based on known ring structures. Another approach is to predict it from scratch based on the principles of quantum chemistry.

• Side chain modeling and optimization

The target sequence fragments are searched in the rotamer database to obtain similar fragments, then their side chain structures are constructed based on the spatial orientation of the fragments, and finally energy minimization is performed to find the lowest energy point, i.e., stable conformation.

• Overall structure optimization

In the 3D models obtained by the above process, there are usually unreasonable contacts between atoms, which need to be eliminated by methods such as simulated annealing and molecular dynamics.

• Structure evaluation

The most commonly used evaluation criterion is the RMSD, which indicates the root mean square deviation of the corresponding atoms of the target and template proteins. It can also be submitted to the SAVES server for validation.

Service Process

Our Features

• For each custom project, we assign a team of expert chemists and biologists to help our partners define their research path and goals.
• We also provide full assistance in realizing the scientific and business plan, as well as delivering the scientific and business plan.
• Creative Enzymes is a leading enzyme technology company offering a trusted suite of services and solutions, especially with our extensive experience in restriction enzyme modification services.

Deliverables

• Related results raw data
• Data analysis
• Image and result analysis
• Results analysis
• Stability assessment report
• Summary of relevant parameters

Why Choose Us?

Creative Enzymes is a professional restriction enzyme homology model generation service provider. We are able to perform individual tests at the most precise level, as well as design and complete a suite of services as a solution to the subject project. Creative Enzymes has accumulated years of quintessence in the field of homology model generation service, helping our clients accelerate drug discovery and development and improve the overall success rate of their projects. If you would like to know more about this service, please feel free to contact us.