Molecular Docking is one of the important methods of molecular simulation, which is essentially a recognition process between two or more molecules that involves spatial matching and energy matching between molecules.
Molecular docking techniques can be used to study the interaction and recognition process between proteins and small molecules. It also enables structure-based drug design and screening by studying the interactions between ligand and receptor molecules and predicting affinity and binding modes. In addition, it has a wide range of applications in areas such as materials design.
Creative Proteomics provides molecular docking of small molecules to proteins and protein-to-protein docking analysis services. Our services enable:
Molecular docking techniques allow molecules from known 3D structural databases to be placed one by one at the active site of the target molecule. By continuously optimizing the position of the receptor compound, its conformation, the dihedral angle of the rotatable bonds within the molecule and the side chains and backbone of the amino acid residues of the receptor, the best conformation for the receptor small molecule compound to interact with the target macromolecule is searched. The binding mode and affinity are predicted, and the ligand with the best affinity to the receptor is selected by scoring function close to the natural conformation.
Molecular docking technique is the main tool used for structure-based drug design. It considers the effect of ligand-receptor binding as a whole, which can better avoid the situation of good local action and poor overall binding that is easy to occur in other methods. In drug design, the molecular docking method is mainly used to search for small molecules with good affinity to the receptor biomolecule from the database of small molecules and perform pharmacological tests to discover new lead compounds from them.
Docking process of proteins and small molecules
Protein docking is a tool to predict protein mutual recognition as well as interactions. Protein docking calculations are achieved by using Protein-DOCK. Protein-DOCK is a rigid protein docking algorithm based on the fast Fourier transform correlation technique. RDOCK is a CHARMm-based energy optimization process that is used to optimize the binding conformations of the protein-protein complexes searched by Protein-DOCK and to score these binding conformations using an energy scoring function.
Protein-to-protein docking process
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