Molecular docking is a type of bioinformatics modeling that involves the interaction of two or more molecules to produce a stable adduct. Molecular docking is an attractive scaffold to understand the interaction of drug and biomolecules for rational drug design and discovery, and to place molecules (ligands) into the preferred binding sites of specific regions of DNA/protein (receptor) targets in mechanism research. It mainly forms stable complexes with potential curative effect and higher specificity in non-covalent form. The information obtained from the docking technique can be used to indicate the binding energy, free energy and stability of the complex. Currently, docking technology is used to predict the tentative binding parameters of ligand-receptor complexes in advance.
Comprehensively utilized docking tools employ search algorithms such as genetic algorithm, fragment-based algorithms, Monte Carlo algorithms and molecular dynamics algorithms. Besides this, some tools such as DOCK, GOLD, FlexX, and ICM are mainly used for high-throughput docking simulations.
Molecular docking can demonstrate the feasibility of any biochemical reaction as it is conducted before the experiment. There are some areas where molecular docking has revolutionized the findings. In particular, the interaction between small molecules (ligand) and protein target (maybe an enzyme) may predict the activation or inhibition of the enzyme. Such type of information may provide the raw material for rational drug designing. Some of the major applications of molecular docking are described below:
Molecular docking can predict an optimized orientation of ligand on its target. It can predict different binding modes of ligand in the groove of target molecule. This can be used to develop more potent, selective and efficient drug candidates [5,7].
Docking in combination with scoring function can be used to evaluate large databases for finding out potent drug candidate in silico, which can target the molecule of interest.
Molecular docking plays an important role in preliminary prediction of the binding properties of drugs and nucleic acids. Medicinal chemists are conducting computer simulation observations, and their main discovery is to predict whether a compound/drug will interact with protein/DNA.
Some basic challenges in docking and scoring are discussed under the following headings.
The preparation of the ligand has a significant impact on the docking result, because the recognition of the ligand by any biomolecule depends on the 3-dimensional orientation and electrostatic interaction.
This is the main challenge in docking or flexible protein handling. Biomolecules/proteins adopt different conformations according to the ligands they bind to.
Another challenge in docking is the imperfect scoring function. Just as the search algorithm has the potential to provide the best conformation, the scoring function should also be able to distinguish the true binding mode from all other parallel modes.
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