- ensure your structure is in a valid PDB format.
- ensure your structure is NOT a multi-domain protein. TABLEAUSearch runs best on single domain proteins as it searches the SCOP (1.71) domain database.
- ensure your structure has only one chain. In case of multiple chains, the server will truncate your query at the first "TER " record in your PDB file.
FAQ-1: I am not sure how to recognize multi-domain proteins?
- visualise your structure using any standard visualization tool.
- choose to represent your protein structure by its backbone.
- A good thumbrule for identifying domains is to look for self-contained, compact folding units within the protein.
FAQ-2: I think I have a multi-domain protein, what do I do?
- create separate PDB files containing each domain for your multi-domain protein.
- you will have to upload these separate PDB (domain) files on the TABLEAUSearch server and submit independent jobs.
FAQ-3: I think I have a domain that involves multiple chains in the PDB. But your server truncates it at the first "TER " record so searches only the first chain. How do I force the server to consider all chains for the search?
- Delete all the intermediate "TER " lines between the chains. The server will then treat all chains as one unit and will search based on that.