Protein Mutation Enhancement

Protein Mutation Enhancement Workflow

Use this skill when the task is to improve a target protein by iterative mutation design. It is an orchestration layer: deterministic library construction, score merging, ranking, and loop-control run locally with stdlib-only helpers; heavyweight model calls run through existing model skills such as fair-esm2 and esmfold2.

Workflow Contract

1. Validate the wild-type protein sequence and define mutable positions.
2. Build a deterministic mutant library:
   • round 1 usually uses single mutants over selected positions;
   • later rounds expand top candidates to doubles or higher-order combinations;
   • every variant has a stable ID such as A12V+G47D.
3. Score sequence effect with an ESM masked-LM model:
   • retrieve fair-esm2 or esmfold2 for concrete GPU recipes;
   • produce a table keyed by id, commonly with esm_delta where higher is better.
4. Predict structures for promising mutants:
   • retrieve esmfold2 for ESMFold2 / ESMFold2-Fast recipes;
   • produce structure metrics keyed by id, commonly plddt, ptm, pae, rmsd_to_wt, or task-specific interface metrics.
5. Merge sequence, structure, property, and functional assay/proxy metrics.
6. Rank by weighted normalized score and apply acceptance thresholds.
7. If any candidate passes thresholds, call host.submit_output(...). If none pass, use the top ranked variants to seed the next loop and expand the library.

Import

The directory name contains hyphens, so import via importlib:

import importlib

pm = importlib.import_module("protein-mutation-enhancement.kernel")

Build a Mutation Library

wt = "MKTAYIAKQRQISFVKSHFSRQ"

library = pm.enumerate_mutants(
    wt,
    positions=[3, 5, 8, 12],
    substitutions={3: ["A", "L", "F"], 5: ["V", "L"], 8: ["R", "K"]},
    max_order=2,
    limit=500,
)

pm.write_fasta(library, "round1_mutants.fasta")

positions are 1-indexed. If substitutions omits a position, all 20 natural amino acids except the wild-type residue are used. Candidate IDs are stable and sorted by position, so downstream score tables can safely join on id.

Merge Scores and Rank

After running ESM and structure jobs, load or construct score tables keyed by variant ID:

esm_scores = {
    "T3L": {"esm_delta": 1.8},
    "Y5V": {"esm_delta": 0.3},
    "T3L+Y5V": {"esm_delta": 2.1},
}
structure_scores = {
    "T3L": {"plddt": 86.0, "rmsd_to_wt": 0.8},
    "Y5V": {"plddt": 71.0, "rmsd_to_wt": 2.4},
    "T3L+Y5V": {"plddt": 82.0, "rmsd_to_wt": 1.1},
}

round_result = pm.run_selection_round(
    library,
    score_tables=[esm_scores, structure_scores],
    weights={
        "esm_delta": 0.45,
        "plddt": 0.25,
        "rmsd_to_wt": 0.15,
        "property_score": 0.15,
    },
    directions={"rmsd_to_wt": "low"},
    acceptance_thresholds={
        "composite_score": 0.72,
        "esm_delta": 1.0,
        "plddt": 75.0,
    },
    top_k=20,
)

best = round_result["ranked"][0]
print(best["id"], best["composite_score"], round_result["should_continue"])

property_score is computed locally from conservative amino-acid-class, hydropathy, charge, and size-change heuristics unless an external table provides it. External assay or task-proxy metrics can be added as extra columns and weights.

Loop Pattern

current_library = pm.enumerate_mutants(wt, positions=active_positions, max_order=1)

for round_idx in range(1, 6):
    # 1. Score `current_library` using fair-esm2 / ESMC.
    # 2. Fold the promising subset using esmfold2 / ESMFold2-Fast.
    # 3. Merge the resulting tables.
    result = pm.run_selection_round(
        current_library,
        score_tables=[esm_scores, structure_scores, function_scores],
        weights=weights,
        directions=directions,
        acceptance_thresholds=thresholds,
        top_k=50,
    )
    if not result["should_continue"]:
        host.submit_output({"accepted": result["accepted"], "round": round_idx})
        break

    active_positions = pm.suggest_next_positions(result["ranked"], max_positions=10)
    current_library = pm.enumerate_mutants(
        wt,
        positions=active_positions,
        max_order=min(round_idx + 1, 4),
        seeds=result["next_round_seeds"],
        limit=2000,
    )
else:
    host.submit_output({"accepted": [], "ranked": result["ranked"][:20]})

Practical Defaults

• Start with curated active-site, binding-site, stability, or conservation positions instead of all positions when possible.
• Use max_order=1 for the first pass, then expand top single mutants into doubles/combinations with seeds=....
• Keep the model jobs separate from ranking artifacts:
  • mutants.fasta
  • esm_scores.csv
  • structure_scores.csv
  • ranked_candidates.json
• Prefer hard acceptance thresholds for safety-critical metrics such as minimum pLDDT or maximum RMSD, and use weighted composite score only after those gates pass.

Notes

• This skill does not claim a mutation is biologically validated. It ranks candidates for follow-up validation using deterministic, inspectable rules.
• Core helpers are pure stdlib and safe for the default offline test suite.
• GPU model installation, weights, and remote execution remain in the model skills (fair-esm2, esmfold2) and compute skills.