I would like to ‘dock’ a ligand that is covalently attached to a Ser active site residue (OG atom). Is it possible to do this using DockingServer?
Docking methods will never result in covalently bound complexes. However, it is still reasonable to try docking in these situations, because the atoms forming the covalent bond should form attractive interactions anyway. The docking result can reflect the real situation, except the bond length of this interaction. If there is no reasonable docking result, you can also consider removing one hydrogen atom from the covalently bound ligand position.
I need my results in excel format, can Althotas do this?
Yes, we export results formatted as SDF files as well as excel and CSV (comma-separated-value). If the results file is too large we will automatically export an excel request as CSV instead.
I want to do further work/viewing/animations related to my docking experiment, can I do this?
Yes, geometry results can be saved in a standard PDB format and are viewable with your favourite molecular visualization software package.
I accidentally deleted a result but do not want to resubmit, can you help?
E-mail support right away, deleting only marks files for deletion on the server, which does not happen right away. If you contact us right away, we may be able to help. Otherwise, I am afraid you will need to re-submit your experiment.
How come <favourite feature> isn’t available?
We are continuously adding new features to our website. Please contact us our make a suggestion on our forum and we will consider the request, it may even be something we are already working on!