AlphaFold 2

Structure prediction with managed databases.

Service-managed flags

The platform fixes critical paths and runtime settings so the container wiring stays stable:

--data_dir, --output_dir, --template_mmcif_dir, --obsolete_pdbs_path
--pdb70_database_path, --uniref90_database_path, --mgnify_database_path
--docker_image_name, --docker_user, --benchmark, --use_precomputed_msas

Example arguments

Select a FASTA under /inputs and supply:

--fasta_paths=/inputs/example.fasta
--model_preset=monomer
--max_template_date=2024-01-01

Swap presets (for example monomer_ptm or multimer) and adjust the template cutoff date as needed.

--max_template_date limits structural templates only. It does not make the sequence/MSA databases time-limited, so treat it as a template-leakage control rather than a full training-data cutoff.

Submit

Start a run from New Job -> AlphaFold 2. Keep inputs under /inputs; outputs are collected from /outputs.