Best is BLAST2GO for functional classification

The basic methodology the software uses are-

1. Blast to nearest NCBI or Uniprot protein.

2. Fetch associated GO terms from NCBI n uniprot databse and KEGG Pathways

Interaction is something else.

Anyways if u can convert your proteins to UNIPROT, go to STRING database for interaction partners.

And if you protein is Human- PIPS database is 4 u

and if mamallian MIPS is there.

More we can tell if you can share origin of your protein.

Best is BLAST2GO for functional classification

The basic methodology the software uses are-

1. Blast to nearest NCBI or Uniprot protein.

2. Fetch associated GO terms from NCBI n uniprot databse and KEGG Pathways

Interaction is something else.

Anyways if u can convert your proteins to UNIPROT, go to STRING database for interaction partners.

And if you protein is Human- PIPS database is 4 u

and if mamallian MIPS is there.

More we can tell if you can share origin of your protein.

You can get domain-centric predictions from the new dcGO resource, which includes dcGO predictor at http://supfam.org/SUPERFAMILY/cgi-bin/dcpredictormain.cgi

Step 1: select 'UP' for UniPathway

Step 2: select 'Amino Acid Sequence' ... or sequence ID if you know it

Step 3: -for uploading multiple sequences at a time-

Step 4: click 'dcGO Predictor'

Enjoy the results.

It also works for all sorts of other ontologies such as GO, phenotype, drug, etc.

1 to try

http://www.protonet.cs.huji.ac.il/

Thanks a lot Saurabh Gayali and specially Dr. Julian Gough. I will try the all the suggestions. Also looking for any structural approach for the same.

Thanks in advance.