Protein-Small Molecule Docking Service

Molecular docking is one of the important methods of molecular simulation. The essence is the recognition process between two or more molecules, which involves spatial matching and energy matching between molecules. Molecular docking methods are widely used in drug design, material design and other fields. The docking software places small molecules at the active site of the target molecule, and finds the receptor by continuously optimizing the position, conformation, dihedral angle of the rotatable bond within the molecule, and the amino acid residue side chain and the backbone of the receptor. The best conformation of the interaction between the small molecule compound and the target macromolecule is determined, and the binding mode and affinity are predicted.

Overall solution

Preparation of receptor structure: construct the three-dimensional structure of the receptor through database download or homology modeling;

• Preparation of drug molecules: download three-dimensional structures of drug molecules through crystal database download or molecular simulation methods;
• Pre-docking processing: processing ligands and receptors, and selecting targets;
• Submit the task: For different systems, select the appropriate docking software and parameters for docking.
• Analysis and graphical results.

Our protein-small molecule docking service

CD ComputaBio' protein-small molecule docking service 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.

CD ComputaBio also provides you with

• Molecule docking service
• Protein-protein docking service

Protein-Small Molecule Docking Service

• • Q: What is the importance of protein-small molecule docking services?

    • A: Protein-small molecule docking service provides a platform for molecular modeling and simulation that helps researchers to investigate protein-ligand interactions. This service can assist in predicting the binding affinity and orientation of a small molecule within a protein's active site, which is crucial in rational drug design. The information that is obtained from protein-small molecule docking service can help researchers to optimize lead compounds, design more potent inhibitors, and develop novel therapeutic interventions.

  • Q: What algorithms could be used in protein-small molecule docking?

    • A: Protein-small molecule docking services rely on several algorithms to predict the binding affinity and orientation of a small molecule within a protein's active site. These algorithms can be broadly categorized into two types: rigid docking and flexible docking.

      Rigid docking algorithms assume that both the protein and the ligand are rigid, and the conformational changes upon binding are minimal. These algorithms are generally fast and suitable for screening large chemical libraries. However, they may miss important binding interactions that occur due to induced fit or conformational changes.

      Flexible docking algorithms, on the other hand, allow for conformational changes in both the protein and the ligand upon binding. These algorithms are generally more accurate than rigid docking algorithms, as they take into account the flexibility of the protein and the ligand. However, they are computationally expensive and require more computational resources.
  • Q: What are the advantages of protein-small molecule docking services?

    • A: Protein-small molecule docking services have several advantages over traditional experimental methods. Firstly, they are faster and more cost-effective than experimental approaches, as they do not require time-consuming and expensive wet lab experiments. Secondly, docking services allow researchers to explore a wider range of chemical space and evaluate a large number of ligands in silico, which is not feasible using traditional experimental methods. Thirdly, protein-small molecule docking services provide insights into the binding mechanism and mode of action, which can be used to guide further experimental studies.