What Is Molecular Docking?
As an important method of computer-aided drug design, molecular docking refers to the process in which two or more molecules recognize each other through geometric matching and energy matching. Scientists use it to simulate the geometric structure and intermolecular forces of molecules with the support of multiple disciplines such as computational chemistry. The essence of molecular docking is the process of mutual recognition between two or more molecules, which involves spatial matching and energy matching between molecules.
Figure 1. Flexible molecular docking. (Dolezal, R.; et al. 2015)
Application of Molecular Docking
- Study the interaction between the ligand (drug molecule) and its receptor (known target protein or active site).
- Predict the binding mode and affinity.
- Discover and optimize drug lead molecules.
Our Molecular Docking Methods
- Rigid docking
In the rigid docking process, the conformation of the molecules participating in the docking does not change, and only the spatial position and posture of the molecules change. We perform rigid docking for molecules with relatively large structures, which are generally used in the preliminary analysis after the model is established.
- Semi-flexible docking
At Alfa Chemistry, semi-flexible docking is mainly applied in the docking between small molecules and large molecules (enzymes or nucleic acids). In the semi-flexible docking process, the conformation of the receptor is rigid and fixed, and only the conformation of the ligand is allowed to change within a certain range, such as the bond angle and bond length of some non-critical parts. We take into account the predictive ability of the model in the entire docking calculation process. Our teams provide a preliminary design plan for the drug molecule by fixing the conformation of the receptor protein and continuously adjusting the chemical structure of the drug molecule.
- Flexible docking
In the flexible docking process, the conformation of the ligand and the receptor is allowed to change freely. We apply flexible docking with high-precision molecular conformation to accurately investigate the recognition between molecules.
Our Molecular Docking Services
- Feature integration
We have designed a multi-feature integration algorithm which is developed based on an algorithm-based matching and a machine learning containing various descriptors.
- Molecular similarity evaluation
Our drug design services but not limited to:
- Homology Modeling
- Ligand/Receptor Calculation
- Binding Pocket Calculation
- Protein Flexibility Prediction
- Ligands Database Project
- Biological Enzyme Catalysis Calculation
Our ligand-based is based on the molecular similarity evaluation between the submitted molecule(s) and those in an active compound database. The database is constituted by multiple reported bioactive molecules with target or mechanism information. We can conduct virtual screening and target prediction based on the two-dimensional and three-dimensional similarity evaluation of molecular structures.
Our Capabilities for Molecular Docking
- Grid docking
In grid docking, the receptor molecule is divided into grid points, and then different types of atoms are used as probes to scan. We can calculate the binding energy of the probe atoms with the receptor on the grid points using the generated gridmap.
- Genetic algorithm
Our teams have designed genetic algorithm combining the semi-flexible docking technology to predict the binding mode of small molecules. Our docking steps are: Determine the bond length and bond angle of the small molecule, then disassemble the small ligand molecule into several rigid fragments, and finally recombine the rigid fragments of the ligand small molecule according to the geometric properties of the receptor surface for conformation search. In terms of energy calculation, we fully consider non-bonding interactions such as electrostatic interaction and van der Waals force.
- Fragment growth method
Alfa Chemistry also provides the fragment growth method to find the best conformation, and selects the best conformation according to the value of the docking free energy. The basic workflow of using fragment growth method for molecular optimization is: First select the core fragment and place it in the correct position of the active site, and then the other parts of the ligand molecule 'grow' on the core structure in turn. A number of optimal ligand and receptor binding forms can be obtained when the ligand growth is over.
Features of Our Molecular Docking
- Accurate spatial conformation and three-dimensional spatial structure
- Correct binding site of the target protein
- Appropriate small molecule database for screening and the correct docking mode
- We provide accurate structural information which is obtained through X-ray crystal diffraction, nuclear magnetic resonance (NMR) methods and homology modeling methods for molecular docking operation.
- Our docking process is fast and effective, which is also can be used for virtual screening of small molecule databases.
Our molecular docking services remarkably reduce the cost, promote further experiments, and accelerate the process of drug design for customers worldwide. Our personalized and all-around services will satisfy your innovative study demands. If you are interested in our services, please don't hesitate to contact us. We are glad to cooperate with you and witness your success!
- Dolezal, R.; et al. Parallel Flexible Molecular Docking in Computational Chemistry on High Performance Computing Clusters. Springer International Publishing. 2015, 418-427.