Protein–Ligand Interaction Modeling Service

The interaction of proteins with ligand molecules is important for many proteins to perform their biological functions. Such interactions are often specific, not only in terms of the protein molecules involved in the interaction, but also in terms of the location where such interactions occur (i.e., the ligand binding site). Now, the bioinformaticians at CD ComputaBio are proud to tell you that we are ready to serve you protein-ligand interaction modeling service!


CD ComputaBio uses a range of methods to simulate protein-ligand interactions, including but not limited to:

Protein–Ligand Interaction Modeling Service

Our team has extensive experience in using these methods to model protein-ligand interactions for drug discovery.

Services Items

  • We perform protein-ligand interaction modeling services through molecular docking, molecular dynamics simulations, and binding free energy calculations.
  • We also provide virtual screening services to identify potential drug candidates from large compound libraries.
  • We provide RMSD, RMSF calculations to determine the stability of the system during the simulation.
  • We provide hydrophobic interaction analysis and binding free energy decomposition analysis to determine the important interaction forces in the protein-ligand binding process.
  • We provide amino acid network interaction analysis to identify significant amino acid contributions and possible mutation sites, etc.

Service Process

We first prepare protein (.pdb) and ligand structures, and then perform molecular docking as well as molecular dynamics simulations. After obtaining the trajectory files, we perform binding free energy calculations to estimate the binding affinity between the protein and the ligand. Finally, we analyze the results to determine the key interactions between the protein and ligand.


  • Raw data
  • Result analysis
  • Relevant parameters and images
  • Key intermolecular interactions
  • Information on other relevant parameters
  • Visualization of protein-ligand complexes (VMD or PyMOL).


  • Identify potential drug candidates
  • Optimize lead compounds
  • Understanding the mechanism of action of existing drugs

Our Advantages

  • Timely delivery of high-quality results
  • Customizable services to meet your specific needs
  • Competitive pricing and flexible payment options
  • High-quality results with rigorous quality control procedures
  • Fast turnaround times to meet tight deadlines
  • Competitive pricing to ensure affordability for all clients

Algorithms and Software

We have access to a range of software tools and computational resources to perform protein–ligand interaction modeling services. This includes molecular docking software such as

  • AutoDock
  • AutoDock Vina
  • Gaussian

Why Choose Us?

CD ComputaBio's protein-ligand interaction modeling service can reduce the cost of post-experiments. Each project needs to be evaluated before we can determine the appropriate analysis plan and price. We can keep up with popular and advanced topics in computational biology science. If you would like to know more about the service pricing or technical details, please feel free to contact us.

* For Research Use Only.