The Gerstein Lab has initially assembled a BLAST database of sequences for all the interacting partners referenced by BioGRID. Then we took the construct sequences for all the NESG solved structures and put them in FASTA format. This file was BLASTed against the BioGRID database with an expectation (e) value of 10-5. The result set was sorted based on the percentage of sequence identity matches. We began to see results at >= 70% with additional results found at >= 50%.
Two reports for example NESG structures which had interacting partners in the BioGRID.
- PDB ID: 2jng
NESG Target ID: HT1
- BioGRID Interacting partners:
- PDB ID: 2jrs
NESG Target ID: HR4730A
We repeated the protocol above with bigger e values of 10-4 and 10-3 which resulted in identical result sets.