Metalloprotein AlphaFold set with enzyme/non-enzyme labeled sites

The AlphaFold set contains computationally generated structures for metalloproteins that were used to test MAHOMES II's enzyme/non-enzyme predictive performance (Feehan et al. 2023).

README.md - Detailed description of AlphaFold set generation.

AF-...-model_v2.pdb - Files with the 3D atomic coordinates of a metalloprotein.

MAHOMES-II_AlphaFold_set_site_data.csv - Contains the data used during the generation of the AlphaFold set for the final sites. Columns are
- Entry: The UniProt accession number of the protein with the bound metal site.
- struc_id: The structures AlphaFold DB name (Febuary 2022) and the name of the file in this directory with added metal site.
- metal_resName: The two letter PDB residue abbreviation for the site's metal
- metal_seqID: The residue index number for the added metal ion.
- Enzyme: The enzyme (True) or non-enzyme (False) label.
- Entry name: UniProt entry name.
- Protein names: The UniProt provided metalloprotein name(s).
- Number of homologs with solved structures (PDB): Number of protein sequences in the PDB (May 21, 2020) with an E-value < 1.
- Number of homologs in MAHOMES II dataset and T-metal-sites10: Number of protein sequences used to train and evaluate MAHOMES II with an E-value < 1 (0 for all entries).
- Metal binding note: UniProt metal binding note that includes information covering the metal’s identity and catalytic flag.
- Metal coordinating residue seqIDs: The sequence indices for the metal coordinating residues included in the UniProt’s metal binding section.