菜单
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.
用 Codex 或 Claude 帮你安装 复制这段 Prompt，粘贴到 Codex、Claude 或其他助手里，让它检查 Skill 页面并帮你完成安装。
基于 SOC 职业分类
Manage lab notebook entries, registry items (plasmids, proteins, etc.), templates, widgets, and audit logs via the Labbook service. Use when creating or viewing lab notebook entries, managing the sample registry, or documenting experiments.
Verify open reading frames (ORFs) in plasmid sequences. Use when the user asks about verifying protein coding sequences, checking if an ORF is present in a plasmid, finding where a protein is encoded, or doing six-frame translation analysis.
Fetch sequencing data from Plasmidsaurus. Use when the user asks about listing sequencing orders, downloading sequencing results, checking order status, or retrieving plasmid sequences from Plasmidsaurus.
Design PCR primers for molecular cloning. Use when the user asks about designing primers, LIC cloning primers, sequencing primers, Gibson assembly primers, or working with NCBI accession codes for cloning.
Calculate protein parameters (MW, pI, extinction coefficient) and generate purification recommendations. Use when the user asks about protein properties, molecular weight, isoelectric point, extinction coefficients, or purification strategies.
Decision trees and workflows for molecular cloning in structural biology labs. Use when the user asks about cloning strategies, LIC vs Gibson, biGBac assembly, tag selection, expression system choice (insect vs E. coli), codon optimization, or designing constructs.
| 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:*) |
Analyze protein sequences to suggest optimal truncation boundaries for recombinant expression constructs, particularly for structural biology (crystallography, cryo-EM).
# Run directly (if built)
cmd/construct_boundary/construct_boundary
# Or via go run
go run cmd/construct_boundary/main.go
# 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
| 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 |
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.
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:
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
{
"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": [...]
}
go run cmd/construct_boundary/main.go --uniprot SETD2_HUMAN --region SET
go run cmd/construct_boundary/main.go --uniprot ENL_HUMAN --min-length 50 --max-length 150
go run cmd/construct_boundary/main.go --sequence "MVLSPADKTN..." --name MyProtein
go run cmd/construct_boundary/main.go --uniprot DOT1L_HUMAN --json > dot1l_boundaries.json
--uniprot to see all suggestions--region to focus on domain of interest--min-length/--max-length based on expression system/primerdesigner skillcd benchaid
go build -o cmd/construct_boundary/construct_boundary cmd/construct_boundary/main.go