Table 2 Three virtual screening methods comparison

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