Sequence Design and Optimization

Sequence Design and Optimization

CD Biosynsis provides professional sequence design and optimization services for synthetic biology researchers around the world to facilitate their cutting-edge research.

Introduction to Sequence Design and Optimization

After protein backbone building, the next step is to generate a sequence that will fold well in the desired topology. The most general and widely used sequence design algorithm in Rosetta is the Packer, which performs a simulated annealing optimization of the side chain placement in a fixed backbone. In order to find the best sequence for a given backbone, fixed backbone sequence design is usually alternated with smaller backbone perturbation and minimization. The iteration of this approach allows the achievement of lower energy structures and more diverse sequences.

Although the Packer is a very powerful side chain optimization algorithm, it is well known that it may be severely affected by the limitations of energy functions and sequence sampling algorithms, which in turn may lead to undesirable/suboptimal design features. To avoid these problems, different strategies have been conceived, such as layer design, consensus loop design, disulfide search, custom selections, to bias the Packer to find the best solutions.

Figure 1. Model-based rotamer repacking and sequence design. (Anand N, et al., 2020)

What We Offer

CD Biosynsis uses advanced bioinformatics tools and calculation methods to provide customers with high-quality sequence design and optimization services.

• Sequence design—Aims to find amino acid identities that minimize the energy function on a fixed protein backbone. During this process, the appropriate sequence is generated and can potentially fold into the desired conformation.
• Sequence optimization—Key step in protein design, which involves designing of the protein sequence that is optimized to ratify the target fold.

Our Advantages

• Advanced and experienced bioinformatics and computational platform.
• The relationship between sequence and structure and/or statistical force field can be collected from the native protein to guide the design of the sequence.
• Experienced technical support and marketing personnel, which can provide customers with pre-sale consultation and technical guidance after sale.
• Provide one-stop services from design to synthesis to meet customers' scientific research needs.

Ordering Process

CD Biosynsis is here to conduct reasonable sequence design and optimization according to customer scientific research requirements, and to provide sequence space search and candidate sequence identification services.

Welcome to contact us for project quotations and more detailed information.

References

1. Poluri K M & Gulati K. Protein engineering techniques: Gateways to synthetic protein universe. Springer, 2016.
2. Anand N, et al. Protein sequence design with a learned potential. bioRxiv, 2020.