What Next After Assigning Function To An Unknown Protein

Question

[rob234king]

I'm working on a fungal pathogen genome which has a number of hypothetical proteins to its genes. I updated the genome and one of the transcripts which had N sequence has now been identified as a uaa transporter by its new pfam domain using interpro.

Is there software methods to take this further and blast it to see if homeologues have some more specific information or if any drugs will antagonise the protein? Is there any recommendations on what may be interesting to do next?

Answer 1

[jackuser1979]

I think you just ran interpro scan and identified new domain. Try blast search with other fungal genomes & genbank nr database, examine if you can find any homologues to your protein sequence. Next you can go for homology modelling, try searching your sequence in PDB database using blast and you can model protein (using swiss-model or any other software- see list of homology modelling software). If you know any drugs to test or you can search through literature and try to find which drug will antagonise your protein. After finding your drug (ligand) you can dock to your protein (receptor) using any one of docking software available-see list of docking software

Answer 2

[Ido Tamir]

something like afterParty? publication: http://www.biomedcentral.com/1471-2105/14/301 website: http://afterparty.bio.ed.ac.uk/study/listPublished