Applications of Protein Structure Modeling

The three-dimensional structure of a protein provides basic information about its biological function and helps design therapeutic drugs that specifically bind to protein targets. In recent years, the number of experimentally determined protein structures has increased dramatically. However, experimental methods are usually tedious and time-consuming. Calculation represents an alternative and supplement to the experimental method for obtaining the three-dimensional structure of the protein.

Protein Structure ModelingFigure 1. Protein structure modeling.

Model Generation

  • Fragment assembly
  • Segment matching
  • Satisfaction of spatial restraints


Protein structure modeling can be applied to determine protein-protein interaction prediction, protein-protein docking, molecular docking, and functional annotation of genes identified in the organism's genome. Even low-precision homology models can be used for these purposes, because their imprecision is often located in loops on the protein surface, and even between closely related proteins.Their variability is usually significant. The functional regions of proteins, especially their active sites, are often more conservative, so modeling can be accurate.

  • Protein structure modeling can also be used to identify subtle differences between related proteins, which have not yet been fully resolved in structure.
  • This method is used to identify the cation binding sites on Na+ / K+ ATPase and put forward hypotheses about the binding affinity of different ATPases.
  • When used in conjunction with molecular dynamics simulations, protein structure modeling can also generate hypotheses about protein dynamics and kinetics, for example, in studying the ion selectivity of potassium channels.


 Applications of Protein Structure Modeling

  • Protein structure modeling saves a lot of labor costs.
  • CD ComputaBio can provide many different modeling services, including antibody modeling and lipid modeling.
  • The calculation cycle is short and fast.
  • The required funds are far less than biological or chemical experiments.
  • The calculation is highly accurate.

Related Services:

CD ComputaBio' protein structure modeling service can significantly reduce the cost of later experiments. Our network analysis service provides accurate approximations of the behavior of real molecules and have proven to be very useful for understanding the different stages of drug development. If you are interested in our services, please contact us for more detailed information.

* For Research Use Only.