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

TYPES OF DOCKING: COVID-19 Docking Server 

The COVID-19 Dock Server web interface is written in HTML and PHP, and JSMol is used for molecular visualization.  
27 targets essential in viral reproduction are available for docking simulation 
The proteins are:  spike protein, membrane protein, envelop small membrane protein, nucleocapsid protein, main protease, papain-like protease, nsp3 (207-379), RNA dependent RNA polymerase (RdRp, nsp12/7/8 complex) , nsp7, nsp8, nsp12, helicase, nsp14, nsp15 (endoribonuclease), nsp10, nsp16, nsp16/10 (2'-O-methyltransferase), nsp1, nsp2, nsp4, nsp6, nsp9, ORF3A, ORF6, ORF7A, ORF8,  and ORF10. 


University of South Florida

Understanding of COVID-19 target-ligand interactions represents a key challenge, particularly in observing the interactions in vitro. To combat this, the 
COVID-19 Docking Server was developed. It is a web server that predicts binding modes between COVID-19 targets and ligands (small molecules, peptides, antibodies, etc). 

In a very short time, many proteins essential to SARS-CoV-2 have been discovered by researchers in China, including the main protease and spike protein in binding with angiotensin-converting enzyme 2 (ACE2) (this is the primary mode of entry that SARS-CoV-2 uses when initiating cell entry).

As of May 2020, 181 structures were released in the Protein Data Bank, which were  related to 11 different kinds of SARS-CoV-2 proteins.

Structures of the other proteins remain unknown, so the modeled structures of SARS-CoV-2 in the dock server are based on the homologous structures of SARS-CoV, due to high amino acid identity between the two coronaviruses (77.2%). 


INTRODUCTION: 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

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