AlphaFold 2

Overview

Protein monomer structure prediction from a typed amino-acid sequence or prepared FASTA.
Protein-only homo- or heteromeric complex modeling when stoichiometry is known.
Comparing homologs, mutants, truncations, or construct boundaries.
Inspecting pLDDT, PAE, pTM, and ipTM before downstream design or simulation.

Modes

Mode	Input shape	When to use it
`single_sequence` Single Sequence Default	Uses a protein sequence entered directly in the form or API parameters.	Predict one typed protein sequence as a monomer.
`custom_input` Custom Input	Uses one selected FASTA file.	Run one supplied protein FASTA as a monomer or multimer.
`batch_monomer` Batch Monomers	Consumes a folder or output set; useful for batches and pipeline handoffs.	Predict every FASTA input in the selected source as a single-chain target.
`batch_multimer` Batch Multimers	Consumes a folder or output set; useful for batches and pipeline handoffs.	Predict every multi-sequence FASTA input in the selected source as one complex.

Canonical Job Configuration

These are the fields exposed by the default job configuration for alphafold2. They are also returned by GET /api/v1/program/params?program=alphafold2 and submitted as the params JSON object to POST /api/v1/job/submit.

Parameter	Type	Modes	What it does
`protein_sequence` Protein Sequence	Protein sequence	Single Sequence	Single-chain protein sequence using standard one-letter amino-acid codes; whitespace is ignored and X is accepted. Required
`target_fasta` AlphaFold FASTA	Input file	Custom Input	Choose one prepared FASTA. A monomer FASTA has one record; a multimer FASTA uses one record per chain. Required; Files: .fasta, .fa, .faa, .fas
`prediction_type` Prediction Type	Text	Custom Input	Choose whether the selected FASTA is a monomer or multimer target. Default: Monomer; Options: Monomer, Multimer
`template_cutoff` Template Cutoff Date	Text	All modes	Only structural templates released on or before this date are considered; sequence databases are not date-limited. Leave blank to use the UTC submission date. Format: YYYY-MM-DD
`msa_search` MSA Search	Text	All modes	Fast uses the reduced database set; Full searches the full database set and is slower. Default: Fast; Options: Fast, Full
`pairwise_confidence` Pairwise Confidence	Yes/no	Single Sequence, Batch Monomers	Use the monomer pTM model to produce PAE/pTM confidence outputs. Default: false
`custom_pairwise_confidence` Pairwise Confidence	Yes/no	Custom Input	Use the monomer pTM model for a custom monomer input. Default: false; Shown when prediction_type is Monomer
`complex_sampling` Complex Sampling	Text	Batch Multimers	Standard runs the usual five seeds per multimer model; Fast runs one seed per model. Default: Standard; Options: Standard, Fast
`custom_complex_sampling` Complex Sampling	Text	Custom Input	Choose sampling depth for a custom multimer input. Default: Standard; Options: Standard, Fast; Shown when prediction_type is Multimer

Advanced configuration fields

Parameter	Type	Modes	What it does
`relaxation` Relaxation	Text	All modes	Relax the top-ranked model, skip relaxation, or relax every model. Default: Best; Options: Best, None, All

Outputs And Metrics

Ranked PDB structures, with the top model usually named like ranked_0.pdb.
Relaxed and unrelaxed structures when relaxation is enabled.
Confidence files and model result files containing pLDDT, PAE, pTM, and multimer interface scores.
pLDDT is per-residue local confidence on a 0-100 scale; above 90 is very high, 70-90 is usually confident, 50-70 is low, and below 50 is often unreliable or flexible.
PAE is predicted aligned error in angstroms; low PAE between domains or chains supports confident relative placement.
pTM summarizes global fold/domain-packing confidence; ipTM focuses on multimer interfaces.

Common Examples

Single enzyme: Single Sequence mode, Fast MSA search, pairwise confidence off, relaxation Best.
Multi-domain protein: Single Sequence mode with pairwise confidence on; inspect PAE before trusting domain arrangement.
Homotrimer: Custom Input with a multimer FASTA containing the sequence three times; use Standard sampling for final review.

Example API params

{
  "mode": "single_sequence",
  "protein_sequence": "MKTAYIAKQRQISFVKSHFSRQDILDLI",
  "msa_search": "Fast",
  "relaxation": "Best"
}

Caveats

AlphaFold 2 does not explicitly model ligands, nucleic acids, cofactors, metals, post-translational modifications, or solvent.
High pLDDT within each chain does not guarantee correct domain-domain or chain-chain orientation.
Template cutoff controls templates, not a complete historical sequence database cutoff.

Advanced Submit

Advanced submit is still available for direct program arguments through POST /api/v1/job/submit-advanced. Prefer canonical configuration unless you need exact low-level arguments or are reproducing a known command line.

Advanced submit accepts AlphaFold command-line flags such as FASTA paths, model preset, template date, MSA/database preset, and relaxation settings.
Use advanced submit for unusual AlphaFold flags or when reproducing an older command line; use canonical configuration for routine jobs.

curl -X POST https://subseq.bio/api/v1/job/submit \
  -H "Authorization: Bearer <api_key>" \
  -F program=alphafold2 \
  -F 'params={"mode":"single_sequence","protein_sequence":"MKTAYIAKQRQISFVKSHFSRQDILDLI","msa_search":"Fast","relaxation":"Best"}'