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Table 2 Three virtual screening methods comparison

From: In silico approach in reveal traditional medicine plants pharmacological material basis

Methods Molecular docking [38] Pharmacophore model [39] Small molecule shape similarity [40]
Theory basis Molecular mechanics, quantum mechanics Statistics Graph theory and other mathematical methods
Overview Obtain the receptor structure information and locate its binding site, mimic the interaction between the receptor and its ligands Establish pharmacophore model, evaluate the matching degree between ligands 3D conformation and pharmacophore models To investigate the structural similarity of unknown molecules by druggable molecules at known targets
Advantages 1. Algorithm is mature
2. A variety of optional softwares
1. High accuracy and efficiency
2. Several commercial pharmacophore databases
1. Fastest screening
2. Abundant data resources
Disadvantages 1. Relatively large amount of calculation
2. Huge data preparation workload
3. Results analysis takes a long time
1. Affected by the quality of pharmacophore model
2. Affected by the amount of protein crystals
1. Low accuracy and rough results
2. Require operator able to develop chemical software