Molecular docking is a method to simulate the interaction between ligand and receptor based on the lock&key principle.
The interaction between ligands and receptors is a process of molecular recognition, mainly including electrostatic interaction, hydrogen bond interaction, hydrophobic interaction, van der Waals interaction, etc. The binding mode and affinity between the two can be predicted by computing.
Wecomput provides professional molecular docking and virtual drug screening services, which can help customers find ligand-protein interactions, explain biological experiments, find new active compounds and provide guidance for compound optimization. The services include protein preparation, active site discovery, protein flexible conformation exploration, ligand conformation database preparation, docking results analysis and evaluation, small molecule compound library preparation, pharmacophore modeling and screening, and personal experience screening.
Molecular docking can be effectively applied to：
- Exploring the interaction mode and binding conformation of drugs and receptors;
- Screening of lead compounds that can bind to targets;
- Explaining the mechanism of drug activity;
- Guiding rational optimization of drug structure.
- homology modeling (lack of receptor structure)
- receptor and ligand preparation
- binding site determination
- protein flexible conformation exploration
- ligand conformation database preparation
- molecular docking
- docking results analysis and evaluate
Molecular docking technology threshold is not high but difficult to master, easy to obtain false positive results. Accurate molecular docking results are inseparable from various knowledge and technical reserves and long-term experience accumulation. Select Wecomput, let the professional do professional things, as long as you provide biological information, we can help you find reasonable binding mode and result analysis.
With the development of X-Ray diffraction and NMR technology, a large number of 3D crystal structures of proteins have been resolved, and the crystal structures of proteins cannot be directly used for molecular docking.In the process of protein resolution, there are often a variety of errors, such as the lack of atoms, the secondary sequence and 3D structure of the protein can not correspond to each other and so on, which will affect the accuracy of docking, especially when these errors occur in the ligand binding pocket. Therefore, these errors must be corrected before docking. The position of heavy atoms without the position information of hydrogen atoms can only be determined through both X-Ray and NMR. Before docking, hydrogenation protonation is needed to mark the local electric property, so as to be used for docking.
After preparing the protein structure, it is necessary to find the active sites of drug binding. The topology of the protein surface is very complex and diverse, and the physical and chemical properties are also very diverse. It is necessary to determine which sites are the positions of small molecule binding and can inhibit or activate the activity of proteins. In fact, there must be some studies and annotations on the biological functions of the target proteins.
In most cases, proteins play their biological functions by binding to natural ligands ( macromolecules or small molecules ). The binding sites of these natural ligands are likely to be the binding sites of their inhibitors or agonists. If there is no biological annotation, the protein surface can also be investigated from multiple perspectives such as topology and physicochemical properties by means of computing and analysis to find the appropriate binding sites, and combine with the experimental information to determine the active sites.
It is well known that there is an inductive-fit effect in the process of protein-ligand interaction, and its conformation will change accordingly in the binding process. The flexibility of the receptors and ligands must be taken into consideration in an accurate docking. Although many of the current software tools claim that flexible docking of receptors can be carried out, there are relatively large limitations in the methods, which may only optimize the conformation of the side chain force field optimization.
We can investigate several different conformations of protein by computer simulation, which can be used as the starting point of docking to consider the flexibility of protein more. Another is the flexibility of the ligand. Although the software automatically considers the flexibility of ligands during docking, such as spinning some spinable bonds. However, the generation of this conformation is also limited, such as the conformation of saturated rings cannot be fully considered. We can traverse the dominant conformation of the ligand as much as possible through conformation search, saturated ring conformation search and other methods as the docking conformation library, so as to improve the accuracy. The docking results are generally sorted by the score of binding free energy.Each ligand may has a variety of binding conformations. The most likely binding mode is selected through comprehensive evaluation methods, such as the score of free energy and the stress energy of molecules, and a truly reasonable binding mode is determined by combining with our judgment.