Usage

Input:

A small molecule (such as a drug or a peptide) in a .pdb or .mol2 file.

The home page of DINC-COVID allows the user to (1) upload the ligand of interest (i.e., pdb or mol2 file), (2) choose parameters (e.g., request preparation of the ligand and select receptor ensemble), (3) provide an e-mail address and (4) submit the job.

Output:

The lowest-energy binding modes of the ligand for each scoring function (Vina, Vinardo, and AutoDock4) and the corresponding receptor conformations as PDB files
The representatives of the largest clusters of ligand conformations and the corresponding receptor conformations as PDB files
A text file containing the energy values for the above results (dincresults.txt)
An interactive visualization for each result using the JSMol Viewer

Sample Results

Input file	Output
ligand	results
ligand	results

Ligand Preparation

If you need so, DINC-COVID can perform the following operations on the ligand you provide.

remove lone pairs
add polar hydrogens and remove non-polar hydrogens
add Gasteiger charges