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