Complexa Binder Design

Complexa Binder Design (workflow)

From one request — "design binders for <target>" — to ranked, independently validated binders. Each returned binder is a co-designed sequence + predicted binder–target complex, gated by interface confidence, by whether the binder actually contacts the target hotspots, and by apo/holo stability.

Generation uses Proteina-Complexa (co-designs binder sequence + full-atom structure together — no inverse-folding step — with reward-guided test-time search). Validation uses a different model family (Boltz2 / OpenFold3), so the headline confidence is an independent check, not the generator grading its own homework.

Upstream model + code (you provide these):

• Project page: https://research.nvidia.com/labs/genair/proteina-complexa/
• Code: https://github.com/NVIDIA-Digital-Bio/Proteina-Complexa (the complexa CLI)
• Weights (NGC): nvidia/clara/proteina_complexa
• Paper: Didi et al., Scaling Atomistic Protein Binder Design…, ICLR 2026.

First time on a host? → references/setup.md — full standalone setup with no NIM: install Proteina-Complexa + download weights, Python deps (numpy biotite pyyaml), AF2 configure-vs-bypass, optional analyze tools (foldseek/sc/dssp), the Boltz2/OF3 validation endpoint, and every env var. Then run bash scripts/check_setup.sh for a one-shot readiness checklist.

Stage 1: Resolve target + hotspots            → target.pdb + hotspots.json   (no GPU)
        ┌──────────────────────────────────────────────────────────────────────┐
        │ repeat until ≥ N validated passers (or a stop cap):                    │
Stage 2 │   Generate (complexa design) → complex .pdb + AF2-reward-gated designs │
Stage 3 │   Validate (Boltz2 default; OF3 optional) → holo+apo + ipTM/ipSAE/     │
        │     pLDDT + apo↔holo RMSD + hotspot contact → passers                  │
        └──────────────────────────────────────────────────────────────────────┘
Stage 4: Report                               → REPORT_<target>_<run>.md (GO/NO-GO)

Composed pieces (read on demand — do not inline)

If you run inside the Proteina-Complexa repo, its bundled .claude/skills (complexa-setup, complexa-target, complexa-design) can drive the generation half; this skill adds the automated Stage 1, the independent validation, GO/NO-GO, and the manifest.

Stage 1 — resolve target and hotspots (no GPU)

The user gives a target as a name, sequence, and/or structure file. Resolve exactly one design-ready structure, in priority order: (1) experimental PDB (RCSB), (2) AFDB model (UniProt → vendor/science-skills/.../fetch_structure.py), (3) user-provided file, (4) fold de novo (MSA-Search + OpenFold3/Boltz2). scripts/pipeline.py:resolve_target_spec/resolve_target automate (1)–(2) from free text.

Hotspots = the target residues the binder should contact — a compact, surface-exposed, binder-accessible epitope. Resolve in evidence order (scripts/hotspot_strategy.py, scripts/pdb_interface.py):

1. PDB co-complex interface (gold standard) — interface residues from a structure where the target contacts a protein partner.
2. UniProt functional residues — Mutagenesis + accessible Active/Binding/Site, filtered to the extracellular/accessible range (catalytic/cytoplasmic pockets are the wrong surface for a binder and are dropped).
3. Literature (Paperclip) — full-text mining when 1–2 are empty (prompts/hotspot_paperclip.md); structure-confirmed to auto-correct numbering.
4. Unconditioned ([]) only as a documented last resort.

Then enforce, deterministically:

• Structure alignment (align_hotspots_to_structure) — drop residues absent from the coordinate file; read back the real 3-letter identity (catches UniProt↔PDB numbering offsets — never assume equal indices or chain A).
• Epitope sanity (_prune_hotspots) — one compact patch: drop outliers > 30 Å from the cluster centroid, cap at 15 residues, prefer ≥ 2.
• Size budget ≤ 500 residues (_crop_target_to_epitope) — Complexa builds an O(n²) pair-feature map over the whole complex, so crop large targets to an epitope window (original numbering preserved).

Preflight (no GPU): python3 scripts/preflight_design.py <name|accession> … reports the conditioned length, re-aligned hotspots + source, compactness, the ≤500 budget, and a READY / NEEDS-ATTENTION verdict. Review before spending GPU.

Stage 2 — generate (Proteina-Complexa, open CLI)

Register the target (hotspots + binder length are target-dict-driven), then use complexa generate (NOT the full complexa design) for the lean, fast path:

python scripts/complexa_design.py run --task-name <name> --run-name <run> \
    --algorithm best-of-n --num-samples <N> --seed 0 --out <run-dir>

complexa_design.py run defaults to the generate verb. With best-of-n + the AF2 reward (AF2 params configured via setup_af2_params.sh + AF2_DIR), the search AF2-selects the best candidates during generation and writes co-designed sequence + structure PDBs to inference/ — use the sequence directly, do not MPNN-redesign it. Search algorithms: best-of-n (default) · beam-search · fk-steering · mcts. Overrides + outputs: references/complexa-cli.md.

Do NOT run the full complexa design for this workflow. Its evaluate stage re-folds every design with AF2/RF3/ESMFold (redundant — best-of-n already AF2-selected during search**)** and its analyze stage needs foldseek/sc (usually not installed). It is much slower and adds a failure mode. The lean generate → independent Boltz2 validation (Stage 3) is the intended path.

No AF2 params? use --af2-bypass (single-pass + drop the AF2 reward); selection then falls entirely to the independent Boltz2 gate (Stage 3). Low-complexity (poly-X) sequences are dropped before spending Boltz2.

Stage 3 — validate (independent refold) + gate

Validate a capped shortlist, not the whole pool. Best-of-n produces many candidates; fold only ~2× the requested N (the top ones by the generation/AF2 reward) — validating the entire pool wastes GPU/time and (on hosted Boltz2) trips rate limits. Point at a local Boltz2 NIM via $BOLTZ2_URL (--endpoint local) when available.

Per binder run two predictions with one refolder (Boltz2 default): holo (binder + target; target MSA, binder single-sequence, write_full_pae) and apo (binder alone). One command does it: scripts/boltz2_refold.py makes the holo calls (with retry/backoff for rate limits) and chains scripts/validate_binders.py, which runs apo + computes the metrics + applies the gate + ranks. Per-chain conditioning + metric definitions: references/validation.md.

Gate (defaults — every gate must hold): ipTM ≥ 0.65, complex pLDDT ≥ 0.70, binder pLDDT ≥ 0.70, apo binder pLDDT ≥ 0.70, ipSAE_min ≥ 0.45, apo↔holo binder RMSD ≤ 2.5 Å, ≥ 20% of conditioned hotspots contacted (CB–CB < 13 Å). Record every design (pass and fail) with a failure_reason. Rank protein binders by interface confidence (ipTM/ipSAE) + pLDDT + stability — not Boltz2 affinity_pic50 (ligand-only).

Bounded-budget loop + report

The deliverable is the top-N binders ranked by interface confidence (default 10). Aim for N that pass the full gate, but bound the cost: run at most 2 generation rounds, then deliver the top-N by score (ipTM, then ipSAE_min) even if fewer than N clear the strict gate — keep each design's pass/failure_reason flag so quality is still visible. Do not keep generating just to chase N strict passes (that is the single biggest time sink). Stop on N-passed / 2 rounds / budget / a zero-passer round. One run dir per campaign; manifest.json records target, Complexa run config + seeds, per-design lineage/scores/artifacts, gate status. The report states GO/NO-GO, requested-vs-achieved N (passed and delivered), ranked binders, and which stop condition fired. Layout, loop, and report sections: references/pipeline.md.

Configuration

• COMPLEXA_REPO — path to your local Proteina-Complexa checkout (the complexa CLI runs there). Checkpoints via the pipeline YAML or ++ckpt_path=…. Reward weights (AF2_DIR, RF3_CKPT_PATH/RF3_EXEC_PATH) via the repo's .env.
• Boltz2 / OpenFold3 endpoints + auth: hosted (https://health.api.nvidia.com/v1/…
  • NVIDIA_API_KEY) or local (http://localhost:8000/…, no auth). The validator takes --endpoint hosted|local; the key is read from NVIDIA_API_KEY/NGC_API_KEY (or --env-file). Never hardcode hosts/keys.
• COMPLEXA_OUTPUTS — run-output root (default ./outputs).

Scripts & assets

• references/setup.md + scripts/check_setup.sh — standalone (no-NIM) install guide and a one-shot environment readiness check.
• scripts/pipeline.py — orchestrator (Stage-1 resolution + open-CLI generation + AF2 gate + scoring); score_existing and full modes.
• scripts/preflight_design.py — no-GPU target/hotspot/size planner.
• scripts/hotspot_strategy.py, scripts/pdb_interface.py — evidence-based hotspots.
• scripts/complexa_design.py — thin complexa design driver + output extraction.
• scripts/setup_af2_params.sh — download AF2-Multimer params (public, no auth) + create the params/ layout, for reward-guided search (best-of-n, etc.).
• scripts/boltz2_refold.py — Stage-3 holo Boltz2 refolds (retry/backoff + throttle) → validation/raw/, then chains validate_binders.py.
• scripts/validate_binders.py — apo Boltz2 + scoring, ipSAE, apo↔holo RMSD, hotspot contact, gating, ranking → ranked_binders.json. Needs the Dunbrack ipSAE script: bash scripts/fetch_ipsae.sh (MIT; fetched, not bundled — see vendor/ipsae/).
• scripts/fetch_target_msa_colabfold.py, scripts/pdb_to_boltz_template_cif.py — target MSA / structural-template helpers for validation.
• vendor/science-skills/ — DeepMind UniProt + AFDB tooling (Apache-2.0) for Stage 1.
• prompts/hotspot_paperclip.md — literature-mining hotspot fallback.
• assets/targets.json — example registered targets (use complexa target add for your own).

Responsible use

De novo binder design is dual-use. Decline requests aimed at enhancing pathogen fitness, toxin potency, or bioweapon function; keep designs to legitimate research and therapeutic intent.

See also

• protein-binder-design — same goal via RFdiffusion + ProteinMPNN (BioNeMo NIMs).
• Proteina-Complexa docs: README.md, docs/INFERENCE.md, docs/CONFIGURATION_GUIDE.md, docs/EVALUATION_METRICS.md, and its bundled .claude/skills/ in the repo above.