protein-engineering-hypothesis

name	protein_engineering_hypothesis
description	Evidence-bounded hypothesis and experiment planning for protein engineering. Use when the user asks what to mutate next, how to prioritize variants, how to falsify a mechanism, or how to design a directed-evolution round. Do NOT invent wet-lab results; chain VenusFactory tools for computational evidence and label model scores as hypotheses.
license	Apache-2.0
metadata	{"version":"1.0","skill-author":"VenusFactory2"}

Protein Engineering Hypothesis

Overview

Instruction-only skill: structure the scientific argument, then point MLS at concrete hub tools. Inspired by scientific-agent-skills hypothesis-generation, adapted to VenusFactory protein tools.

VenusFactory execution

1. Load this skill.
2. Produce a short plan with: Observation → Hypothesis → Computational test → Wet-lab falsifier.
3. Execute tests via other skills/tools (do not reimplement).

Recommended evidence chain

Question	Skills / tools
What is known about the protein?	uniprot_database, interpro_domain_annotation, pubmed
Where is it expressed?	hpa_expression_context
Structure confidence?	protein_structure_pipeline / alphafold_database
Which mutations look beneficial?	zero_shot_mutation_workflow
Redesign backbone-constrained seq?	proteinmpnn_design_workflow
Kinetics / EC?	brenda_database
Partners / pathways?	string_database, kegg_database
Train a custom head?	venus_finetune_workflow

Output template (for CB/MLS)

### Observation
...
### Hypothesis (falsifiable)
...
### Computational tests (ordered)
1. tool/skill … success = …
### Predicted outcome
...
### Wet-lab falsifier (suggested, not executed here)
...
### Risks / confounders
- Model score ≠ experimental activity

Rules

• Never present zero-shot / PLM ranks as measured ΔΔG or activity.
• Prefer protecting catalytic residues (interpro + literature) before design.
• End computational rounds with at least one figure when numeric tables exist.

When NOT to use

• User only wants a single tool call with no scientific framing — call that tool's skill directly.