constructboundary - SKILL.md Agent Skill

name: constructboundary description: Predict optimal construct boundaries for protein expression. Use when the user asks about domain boundaries, construct design, truncations, which region of a protein to express, or identifying disordered regions. allowed-tools: Bash(construct_boundary:*)

Construct Boundary Predictor

Analyze protein sequences to suggest optimal truncation boundaries for recombinant expression constructs, particularly for structural biology (crystallography, cryo-EM).

CLI Location

# Run directly (if built)
cmd/construct_boundary/construct_boundary

# Or via go run
go run cmd/construct_boundary/main.go

Quick Start

# By UniProt ID
go run cmd/construct_boundary/main.go --uniprot CHD1_HUMAN

# By gene name
go run cmd/construct_boundary/main.go --uniprot CHD1

# Focus on specific region
go run cmd/construct_boundary/main.go --uniprot CHD1_HUMAN --region 1400-1600

# Focus on domain by name
go run cmd/construct_boundary/main.go --uniprot CHD1_HUMAN --region CHCT

Options

Option	Description
`--uniprot`	UniProt ID, entry name (CHD1_HUMAN), or gene name
`--sequence`	Raw amino acid sequence (alternative to --uniprot)
`--name`	Protein name (required with --sequence)
`--region`	Focus region: "500-800" or domain name like "ATPase"
`--min-length`	Minimum construct length in aa (default: 100)
`--max-length`	Maximum construct length in aa (0 = no limit)
`--json`	Output as JSON for programmatic use
`--plot`	Write ASCII visualization to file

Data Sources

The tool fetches and integrates data from:

Source	Data
UniProt	Sequence, domains, active sites, PTMs, secondary structure
AlphaFold DB	Per-residue pLDDT confidence scores
PDB	Existing crystallized/cryo-EM construct boundaries

Data is cached in ~/.cache/benchaid/ for 30 days.

Scoring Algorithm

Boundaries are scored (0-100) based on:

Factor	Weight	Criteria
Disorder transition	+30	Boundary at disorder→order transition
Domain boundary	+25	Aligns with Pfam/UniProt domain
Loop region	+20	Low pLDDT flanked by high pLDDT
Structured side	+15	pLDDT > 70 on the construct interior
PDB match	+10	Matches existing structure boundary

Penalties:

Cuts α-helix or β-strand: -50
Near active site: -100
Within 5 residues of PTM: -20

Output Format

Text Output (default)

CONSTRUCT BOUNDARY PREDICTIONS FOR CHD1_HUMAN (1710 aa)
========================================================

Rank  Region        Length  Score  Rationale
----  ------------  ------  -----  ---------------------------------
1     1431-1510     80      94     domain boundary; high pLDDT side
2     270-443       174     89     domain boundary; PDB boundary
3     614-900       287     85     disorder transition; loop-like region

DISORDERED REGIONS (pLDDT < 50):
  1-45
  168-265
  1520-1710

EXISTING PDB STRUCTURES:
  4O42: 1431-1506 (1.9 Å)
  2EJK: 270-440

Position: |-------------------|-------------------|-------------------|-------------------|
pLDDT:    ..=###==============###==========================================###...........
Disorder: ##....##############...................................................#########
Domains:       ====           ==========================================     ====
Suggested:     1111           22222222222222222222222222222222222222222      3333

JSON Output (--json)

{
  "protein": {
    "uniprot_id": "O14646",
    "name": "CHD1_HUMAN",
    "length": 1710,
    "gene": "CHD1"
  },
  "predictions": [
    {
      "rank": 1,
      "start": 1431,
      "end": 1510,
      "length": 80,
      "score": 94,
      "rationale": "domain boundary, high pLDDT side",
      "evidence": {
        "pdb_match": "4O42",
        "domain": "CHCT",
        "avg_plddt": 89.2,
        "disorder_fraction": 0.02
      }
    }
  ],
  "features": {
    "domains": [...],
    "disordered_regions": [...],
    "pdb_structures": [...],
    "plddt_scores": [...]
  },
  "warnings": [...]
}

Examples

Design construct for a specific domain

go run cmd/construct_boundary/main.go --uniprot SETD2_HUMAN --region SET

Find minimal construct with length constraints

go run cmd/construct_boundary/main.go --uniprot ENL_HUMAN --min-length 50 --max-length 150

Analyze custom sequence

go run cmd/construct_boundary/main.go --sequence "MVLSPADKTN..." --name MyProtein

Export for downstream processing

go run cmd/construct_boundary/main.go --uniprot DOT1L_HUMAN --json > dot1l_boundaries.json

Typical Workflow

Initial scan: Run with just --uniprot to see all suggestions
Refine: Use --region to focus on domain of interest
Constrain: Add --min-length/--max-length based on expression system
Design primers: Use top predictions with /primerdesigner skill

Limitations

pLDDT-based disorder detection (IUPred not integrated)
Secondary structure from UniProt annotations only (PSIPRED not integrated)
No coiled-coil or transmembrane prediction
Requires network access for UniProt/AlphaFold queries (uses cache)

Building

cd benchaid
go build -o cmd/construct_boundary/construct_boundary cmd/construct_boundary/main.go