Therapeutic Protein Designer

AI-guided de novo protein design using RFdiffusion backbone generation, ProteinMPNN sequence optimization, and structure validation for therapeutic protein development.

KEY PRINCIPLES:

1. Structure-first - Generate backbone geometry before sequence
2. Target-guided - Design binders with target structure in mind
3. Iterative validation - Predict structure to validate designs
4. Developability-aware - Consider aggregation, immunogenicity, expression
5. Evidence-separated - Report folding, pose, geometry, protonation and experimental evidence independently
6. Actionable output - Provide sequences ready for experimental testing
7. English-first queries - Always use English terms in tool calls

Therapeutic protein design starts with the target interaction. What binding surface do you need to cover? A small pocket = nanobody or peptide. A large flat surface = designed protein. Stability, immunogenicity, and manufacturability constrain the design space.

LOOK UP, DON'T GUESS

When uncertain about any scientific fact, SEARCH databases first rather than reasoning from memory. A database-verified answer is always more reliable than a guess.

---

COMPUTE, DON'T DESCRIBE

When analysis requires computation (statistics, data processing, scoring, enrichment), write and run Python code via Bash. Don't describe what you would do — execute it and report actual results. Use ToolUniverse tools to retrieve data, then Python (pandas, scipy, statsmodels, matplotlib) to analyze it.

When to Use

Apply when user asks to:

• Design a protein binder, therapeutic protein, or scaffold
• Optimize a protein sequence for function
• Design a de novo enzyme
• Generate protein variants for target binding

---

Workflow Overview

Phase 1: Target Characterization
  Get structure (PDB, EMDB cryo-EM, AlphaFold), identify binding epitope

Phase 2: Backbone Generation (RFdiffusion)
  Define constraints, generate >= 5 backbones, filter by geometry

Phase 3: Sequence Design (ProteinMPNN)
  Design >= 8 sequences per backbone, sample with temperature control

Phase 4: Structure Validation (ESMFold/AlphaFold2)
  Predict structure, compare to backbone, assess pLDDT/pTM

Phase 5: Developability Assessment
  Aggregation, pI, expression prediction

Phase 6: Report Synthesis
  Ranked candidates, FASTA, experimental recommendations

---

Critical Requirements

For iterative campaigns, conflicting predictions, glycosylated receptor checks, conditional pH binding, or competition preparation, use Protein Design Campaign alongside this workflow. Verify installed tool schemas before executing examples; model confidence and successful execution do not establish binding.

Report-First Approach (MANDATORY)

1. Create [TARGET]_protein_design_report.md first with section headers
2. Progressively update as designs are generated
3. Output [TARGET]_designed_sequences.fasta and [TARGET]_top_candidates.csv

Design Documentation (MANDATORY)

Every design MUST include: Sequence, Length, Target, Method, and available Quality Metrics (pLDDT, pTM, MPNN score, binding prediction). Mark unavailable metrics unmeasured or uncomputed; do not fabricate binding predictions or experimental values.

---

NVIDIA NIM Tools

Tool	Purpose	Key Parameter
NvidiaNIM_rfdiffusion (requires NVIDIA_API_KEY env var; free key at build.nvidia.com)	Backbone generation	contigs + input_pdb (both required), diffusion_steps (NOT num_steps; default 15)
NvidiaNIM_proteinmpnn (requires NVIDIA_API_KEY env var; free key at build.nvidia.com)	Sequence design	input_pdb (required; NOT pdb or pdb_string), num_seq_per_target, sampling_temp (a list)
ESMFold_predict_structure	Fast validation	sequence (NOT seq)
NvidiaNIM_alphafold2 (requires NVIDIA_API_KEY env var; free key at build.nvidia.com)	High-accuracy structure inference from sequence	sequence, algorithm
NvidiaNIM_esm2_650m (requires NVIDIA_API_KEY env var; free key at build.nvidia.com)	Sequence embeddings	sequences, format

Common Parameter Mistakes

Tool	Wrong	Correct
NvidiaNIM_rfdiffusion (requires NVIDIA_API_KEY)	num_steps=50	diffusion_steps=50 (plus required contigs and input_pdb)
NvidiaNIM_proteinmpnn (requires NVIDIA_API_KEY)	pdb=content or pdb_string=content	input_pdb=content
ESMFold_predict_structure	seq="MVLS..."	sequence="MVLS..."
NvidiaNIM_alphafold2 (requires NVIDIA_API_KEY)	seq="MVLS..."	sequence="MVLS..."

NVIDIA NIM Requirements

• API Key: NVIDIA_API_KEY environment variable required
• Rate limits: 40 RPM (1.5 second minimum between calls)
• AlphaFold2 may return 202 (polling required); RFdiffusion and ESMFold are synchronous

---

Supporting Tools

Tool	Purpose	Key Parameters
PDBe_get_uniprot_mappings	Find PDB structures	uniprot_id
RCSBData_get_entry	Download PDB file	pdb_id
alphafold_get_prediction	Get AlphaFold DB structure	accession
EMDB_search_structures	Search cryo-EM maps	query
EMDB_get_structure	Get entry details	entry_id
UniProt_get_entry_by_accession	Get target sequence	accession
InterPro_get_protein_domains	Get domains	accession

---

Folding and Developability Screening

These are illustrative computational screening tiers, not binding-evidence grades or calibrated success probabilities. Benchmark screening with appropriate controls. Monomer pLDDT/pTM cannot establish a complex pose, affinity, cross-species binding or pH selectivity. Report those dimensions separately, including missing evidence.

Tier	Criteria
T1 (strongest in this screen)	pLDDT >85, pTM >0.8, low aggregation, neutral pI
T2	pLDDT >75, pTM >0.7, acceptable developability
T3	pLDDT >70, pTM >0.65, developability concerns
T4	Failed validation or major developability issues

---

Completeness Checklist

• Target structure obtained (PDB or predicted)
• Binding epitope identified
• >= 5 backbones generated, top 3-5 selected
• >= 8 sequences per backbone, MPNN scores reported
• All sequences validated (ESMFold), pLDDT/pTM reported, >= 3 passing
• Developability assessed (aggregation, pI, expression)
• Ranked candidate list, FASTA file, experimental recommendations

---

Reference Files

• DESIGN_PROCEDURES.md - Phase-by-phase code examples, sampling parameters, fallback chains
• TOOLS_REFERENCE.md - Complete tool documentation with code examples
• EXAMPLES.md - Sample design workflows and outputs
• CHECKLIST.md - Detailed phase checklists and quality metrics
• design_templates.md - Report templates and output format examples