For small molecule docking, Autodock Vina is used as docking engine, and Open Babel was used for format transformation or a 3D coordinate generation. 

Figure A is an example of small molecule docking. The RdRp is shown to have docked with its inhibitor. The experimental structure of RdRp with its inhibitor is
colored in gray. The predicted structure of Top 1 is colored in pink. 

University of South Florida

- Small molecule docking 
- Experimental complex structure docking 
- homology modeled- structure docking 
- antibody and peptide docking 

TYPES OF DOCKING: COVID-19 Docking Server 

Kong, R., Yang, G., Xue, R et al. COVID-19 Docking Server: A meta server for docking small molecules, peptides and antibodies against potential targets of COVID-19.  Bioinformatics. 2020. doi:10.1093/bioinformatics/btaa645
https://academic.oup.com/bioinformatics/article/doi/10.1093/bioinformatics/btaa645/5874442

COVID-19 Docking Server: A meta server for docking small molecules, peptides and antibodies against potential targets of COVID-19

Small molecule docking: COVID-19 Docking Server 

For experimental structures, the docking box was set on the center of the ligand with 30Å×30Å×30Å in length to include the residues of the entire cavity.  
In Figure B, the image shows an example of small molecule batch docking. The crystal structure of main protease is colored gray and the predicted binding poses of 11 inhibitors are shown in different colors. 

Experimental complex structure docking: COVID-19 docking server

For homology modeled structures, it is defined according to the active sites or binding sites of its homologs of SARS-CoV. 
Figure  C shows an example of peptide docking. The post-fusion state of S2 segment of spike protein docked with a helical peptide. The 6-helices structure of S2 is colored in gray. The predicted structure of Top 1 is colored in pink. 

Homology-modeled structure docking: COVID-19 docking server

For peptide and antibody structures, CoDockPP is used as a docking engine. 
CoDockPP program provides a multistage FFT-based strategy for both global docking and site-specific docking. 
 An angle interval of 15º is used for rotational sampling, and a spacing of 1.2 Å is adopted for fast Fourier transform (FFT) translational search. 
The top binding modes are clustered with ligand root mean square deviations (L_RMSD) cutoff of 3.0 Å in global docking and 2.0 Å in site-specific docking.

Figure D shows an example of antibody docking. The spike protein docked with antibody. The spike protein is colored in gray and the predicted structure of Top 1 is colored in pink.

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