search

haddocking / arctic3d

Automatic Retrieval and ClusTering of Interfaces in Complexes from 3D structural information
Apache License 2.0
27 stars 6 forks source link

renumbering haddock pdbs according to uniprot? #76

Closed mgiulini closed 1 year ago

mgiulini commented 2 years ago

renumbering input pdbs according to a specific uniprot numbering can be quite painful. I wrote a script for that, should we include it in the benchmark? may it be useful in other contexts?

rvhonorato commented 2 years ago

I think its quite useful to have the PDBs match the canonical numbering! Goes into the line of input standardization.

amjjbonvin commented 2 years ago

Aren’t the mmCIF files now also providing it?

mgiulini commented 2 years ago

Aren’t the mmCIF files now also providing it?

They are indeed, I didn't know it! I guess this could remove arctic3d hard dependency on the pdbrenum web server.

1 A 1 7 GLY G G 51 P49137 1 1 ? y 1 CATH 3.30.200.20 2ozaA01 1 1
1 A 2 7 GLY G G 51 P49137 1 1 ? y 1 SCOP2 8031356 SCOP2-FA 1 1
1 A 3 7 GLY G G 51 P49137 1 1 ? y 1 SCOP2 8043734 SCOP2-SF 1 1
1 A 1 8 LEU L L 52 P49137 1 1 ? y 1 CATH 3.30.200.20 2ozaA01 1 1
1 A 2 8 LEU L L 52 P49137 1 1 ? y 1 SCOP2 8031356 SCOP2-FA 1 1

There's a lot of information in these updated files!