Guide to use
In order to use Intercalate, user needs to input a DNA 3D structure (in RCSB PDB file format) or the DNA sequence with information about the intercalation site. MD DNA is generated from the DNA sequence due to its higher accuracy. Now, upload the hydrogens added ligand/intercalator molecule which needs to be docked and enter its formal charge. Ligand should be a non-metallo molecule, having planarity to some extent and should be in a PDB file format. User can optionally feed the email address to receive the result once the job is completed. Lastly, click on Intercalate button for submitting the job. Lack of planarity in ligand may lead to job failure. Also, the user is required to check atom labels. Improperly named atoms may lead to errors.