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

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.

Figure 1. 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

• 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

CD ComputaBio also provides you with

• Molecule docking service
• Protein-Small Molecule Docking Service

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.

Protein-Protein Docking Service FAQs

• • Q: What algorithm is used in protein-protein docking?

    • A: The algorithm of protein-protein docking involves predicting the binding mode and energy of two or more protein molecules based on their 3D structures. The process typically involves several steps, including rigid-body docking, refinement, scoring, and analysis.

  • Q: What is the application of protein-protein docking?

    • A: protein-protein docking techonoly has the following applications:

      Hit identification: molecular docking combined with a scoring function can be applied to quickly screen large databases of potential in silico to identify molecules that are possible to bind to protein target of interest.

      Lead optimization: molecular docking can be applied to predict the binding mode of a ligand binding to a protein. This information may in turn be applied to design more potent and selective analogs

      Bioremediation: molecular docking can also be used for the prediction of pollutants that can be degraded by enzymes.

      Characterization of the binding mode also plays a significant role in elucidating fundamental biochemical processes.
  • Q: What software is available for protein docking?

    • A: ZDock, ClusProh and Rosetta can be used for protein-protein docking. ZDock is a fast and efficient docking program that uses shape complementarity to generate initial models. based docking program that uses scoring functions based on energy minimization and Monte Carlo simulations.

  • Q: What are the advantages of the protein-protein docking service?

    • A: Protein-protein docking service has the following advantages:

      Protein-protein docking is able to predict the interaction between two or more protein molecules independent of experimental data.

      Protein-protein docking services can also provide insights into the structural features and molecular interactions that drive protein-protein interactions.

      Protein-protein docking services can help design novel therapeutics for specific protein targets.

      In addition In addition, protein-protein docking services can help identify potential drug targets and assist in optimizing lead compounds and drug candidates
  • Q: What are the protein-protein docking service items?

    • A: Protein-protein docking services typically offer several programs, including interaction details, energy analysis, qing'jian hydrogen bonding analysis, etc. Some protein-protein docking services may also offer additional features such as clustering analysis, energy minimization, and cross-docking experiments.