Small-molecules bind to proteins within surface cavities. The prediction of these interactions is done through docking simulations. Structure-based virtual screening (molecular docking) has been used to discover new ligands based on target structures. Docking methods are widely applied and accepted nowadays in drug design. Two approaches are particularly popular within the molecular docking community. One approach uses a matching technique that describes the protein and the ligand as complementary surfaces. The second approach simulates the actual docking process in which the ligand-protein pairwise interaction energies are calculated. Both approaches have significant advantages as well as some limitations.
Table 1 Molecular docking software (Pedro H. M. Torres, et al. 2019)
Various docking software is under developed that will increase the biological accuracy in modeling docking processes. Researchers and pharmaceutical companies can use open-source software to speed up simulations to rank small molecules and focus on specific protein families that are important in drug R & D. Predicting interactions between proteins and ligands using computer-aided methods or artificial intelligence (AI) models has attracted great interest in recent years. Deep learning paired with drug docking and molecular dynamics simulations identify small molecules to identify with precision the correct ligand conformation within the binding pocket of a given target molecule.
Figure 1 Overview of Molecular Docking
To perform a successful docking screen, the first requirement is a structure of the protein of interest. Usually the structure has been determined using a biophysical technique such as x-ray crystallography, NMR spectroscopy or cryo electron microscopy (cryo-EM), but can also derive from homology modeling construction. This protein structure and a database of potential ligands serve as inputs to a docking program. The success of a docking program depends on two components: the search algorithm and the scoring function. Here, we introduce several molecular docking software with brief tutorials.
rDock is a fast and universal open source docking program that can be used to dock small molecules with proteins and nucleic acids.Learn More
DOCK 6 is written in C++, and is functionally divided into independent components, thus having a high degree of program flexibility.Learn More
Molecular docking is to place the ligand molecule at the active site of the receptor, and then evaluate the interaction between the ligand.Learn More