We have a large number of PDB files generated by AlphaFold (essentially CATH / Pfam domain assignments). We want to make these available via 3D-beacons client implementation.
We want to be able to automatically generate the required meta-data files by extracting data from:
file name (eg arabidopsis_thaliana/AF-A0A140JWM8-F1-model_v1.pdb)
data in the REMARK section
REMARK CATH AF_MODEL /SAN/cath/cath_v4_3_0/alphafold/species/cleaned/arabidopsis_thaliana/AF-A0A140JWM8-F1-model_v1.pdb
REMARK CATH CATH_SFAM_ID 1.10.630.10
REMARK CATH EVALUE 0.0
REMARK CATH MATCH c3106fcb1d43b5aed0678513f9d73d54/24-470
REMARK CATH PFAM_ID N/A
REMARK CATH QUERY c3106fcb1d43b5aed0678513f9d73d54
ATOM 195 N HIS A 24 -22.980 -13.274 22.072 1.00 84.31 N
ATOM 196 CA HIS A 24 -22.861 -12.577 20.796 1.00 84.31 C
ATOM 197 C HIS A 24 -23.941 -11.494 20.653 1.00 84.31 C
ATOM 198 CB HIS A 24 -22.913 -13.616 19.672 1.00 84.31 C
The intention is to add a script to the code base that is able to do this.
We have a large number of PDB files generated by AlphaFold (essentially CATH / Pfam domain assignments). We want to make these available via 3D-beacons client implementation.
We want to be able to automatically generate the required meta-data files by extracting data from:
arabidopsis_thaliana/AF-A0A140JWM8-F1-model_v1.pdb)REMARKsectionThe intention is to add a script to the code base that is able to do this.