ProtClean FAQ
My protein structure is missing loops and residues, is that a problem?
No, ProtClean integrates AI methods to fill in missing portions of your protein structure (provided the sequence is known)
How do I know whether I should remove or retain cofactors?
ProtClean allows you to view every cofactor and non-solvent small molecule in your uploaded structure within the 3D structure of the protein. You can select the molecules to retain and ProtClean automatically removes the rest. This gives you the context to retain necessary cofactors and discard unnecessary crystallization artifacts.
Does ProtClean support membrane-bound proteins?
Yes. ProtClean can be used to generate an explicit membrane model to accompany an input protein.
What kinds of membranes can I generate for my membrane-bound protein with ProtClean?
ProtClean generates a fully atomistic membrane for your membrane-bound receptors and equilibrates it in just a few hours. Membranes of many thicknesses are supported, including the common POPC, DLPE, and DOPC models.
I prefer to prepare my protein with a different program. Can I import the prepared protein from this program instead of using the ProtClean tool?
Yes. Using the QSimulate ProtClean tool is optional. If you have a fully prepared protein, then you can import it directly into QUELO or QuValent.