Protein-Protein Docking Service

Protein-Protein Docking Service

The interaction between proteins is essential. It is the basis of all metabolic activities of the cell. In order to better understand the biological activity of cells, the function of protein monomers and complexes must be well understood, which will involve the study of protein interactions. Recognizing and studying protein-protein docking is an important research content in life sciences. Drug molecules used to treat diseases usually regulate or block protein-protein interactions, so protein-protein interaction sites also represent an important class of drug targets. Computational methods can well supplement the experimental determination of the structure of complexes when studying protein docking.

Classifications of our protein-protein docking service

Classifications Features
Bound docking

The protein structure used in the docking comes from the complex they form.

Unbound docking

The protein structure used in unbound docking comes from the monomer structure when they are not bound to other proteins in most cases. One difficulty of unbound docking is the change of protein conformation.

Data-guided protein-protein docking process

  • Definition of protein rotation degree of freedom and setting of mutual recognition.
  • Selection of search methods for protein-protein interactions.
  • Fine optimization and cluster analysis.
  • Prediction of protein-protein complex binding patterns.

Protein-protein docking process.Figure 1. Protein-protein docking process.

Data-guided protein-protein docking process

Data-guided protein-protein docking process

  • Random rotation, rigid body energy optimization.
  • Simulated annealing of semi-rigid body in torsion angle space.
  • Energy optimization in Cartesian space using the displayed solvent model.
  • Clustering conformation with RMSD of the interface residue main chain.
  • Analyze and sort clusters according to the average interaction energy of clusters (electrostatic energy, van der Waals energy, fuzzy interaction constraint energy) and average embedding surface area.

High-resolution protein-protein docking process

High-resolution protein-protein docking process

  • Create protein-protein complexes from protein monomers, considering the flexibility of the model side chains.
  • An explicit model of the atomic details of the protein-protein interface, considering the flexibility of the entire complex.
  • Energy optimization after fine optimization.
  • Perform flexible docking or ensemble docking.
  • The complex combines model prediction and result evaluation.

Our services

Project Name Protein-Protein Docking Service
Samples requirement Our protein-protein docking service requires you to provide specific docking requirements.
We can offer you with the following services but not limit to:
  • Data-guided protein-protein docking
  • High-resolution protein-protein docking process
Timeline Decide according to your needs.
Deliverables We provide you with raw data and calculation result analysis service.
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CD ComputaBio also provides you with

CD ComputaBio' protein-protein docking is the main method used in structure-based drug design. This technology is to place the ligand molecule in the position of the active site of the receptor molecule, and then in real time according to the principles of geometric complementation, energy complementation and chemical environment complementarity. Evaluate how well the ligand interacts with the receptor, and find the best binding mode between the two molecules. In drug design, the molecular docking method is mainly used to search for small molecules with good affinity with the receptor biomacromolecule from the small molecule database, and conduct pharmacological tests to discover new lead compounds. If you have service needs for molecular docking, please feel free to contact us.

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