Protein structure analysis
Protein structure analysis skill. PDB structure retrieval, structural alignment (TM-align), binding site analysis, and structure-function relationship exploration.
Use This Skill When
- PDB structure retrieval.
- Structural alignment (TM-align).
- Binding site analysis.
- Structure-function relationship exploration.
Required Inputs
- Research objective, decision target, or hypothesis.
- Available data, source constraints, and domain assumptions.
- Required outputs, success metrics, and deadline or reproducibility constraints.
Workflow
- Confirm scope, assumptions, and the exact artifact set to save.
- Apply the narrowest domain method that answers the request with defensible evidence.
- Save code, tables, figures, and intermediate outputs to files instead of chat-only output.
- State limitations, uncertainty, and any validation or sensitivity checks performed.
- Append skill selection, handoff I/O, and file writes to
logs/process-log.jsonl.
Deliverables
report.md: concise method, results, interpretation, and file inventory in the user's language.results/: structured outputs, metrics, model artifacts, or extracted findings.figures/: English-only charts, diagrams, or panels when visual output is needed.data/: processed or derived datasets when transformation occurs.
Available Tools (MCP)
External tools available via ToolUniverse MCP server.
Falls back to Python requests + public REST APIs when MCP is unavailable.
| Source |
Tool |
Description |
| RCSB PDB |
RCSB_search |
RCSB PDB API |
| RCSB PDB |
RCSB_get_structure |
RCSB PDB API |
| UniProt |
UniProt_get_entry |
UniProt API |
Quality Gates
If any gate fails: identify the specific failing check, fix the issue, and re-validate before proceeding.
Gotchas
- PDB structures may contain missing residues or alternate conformations. Check structure completeness before analysis
- Docking scores are relative, not absolute binding affinities. Use for ranking, not predicting Kd values
- Protein identifiers differ across databases (UniProt, PDB, RefSeq). Map to a canonical namespace before integration
Validation Loop
- Execute analysis and generate outputs
- Check:
- Method selection matches the research question and stated assumptions
- All outputs are saved to files (no chat-only results)
- Limitations and uncertainty are explicitly stated
logs/process-log.jsonl is updated with execution trace
- If any check fails:
- Identify the failing gate
- Fix the specific issue
- Re-run validation
- Proceed only after all gates pass
1---2name: co-scientist-protein-structure-analysis3description: Protein structure analysis skill. PDB structure retrieval, structural alignment (TM-align), binding site analysis, and structure-function relationship exploration. Use when working with pdb structure retrieval, structural alignment (tm-align), binding site analysis.4---56# Protein structure analysis78Protein structure analysis skill. PDB structure retrieval, structural alignment (TM-align), binding site analysis, and structure-function relationship exploration.910## Use This Skill When1112- PDB structure retrieval.13- Structural alignment (TM-align).14- Binding site analysis.15- Structure-function relationship exploration.1617## Required Inputs1819- Research objective, decision target, or hypothesis.20- Available data, source constraints, and domain assumptions.21- Required outputs, success metrics, and deadline or reproducibility constraints.2223## Workflow24251. Confirm scope, assumptions, and the exact artifact set to save.262. Apply the narrowest domain method that answers the request with defensible evidence.273. Save code, tables, figures, and intermediate outputs to files instead of chat-only output.284. State limitations, uncertainty, and any validation or sensitivity checks performed.295. Append skill selection, handoff I/O, and file writes to `logs/process-log.jsonl`.3031## Deliverables3233- `report.md`: concise method, results, interpretation, and file inventory in the user's language.34- `results/`: structured outputs, metrics, model artifacts, or extracted findings.35- `figures/`: English-only charts, diagrams, or panels when visual output is needed.36- `data/`: processed or derived datasets when transformation occurs.3738## Available Tools (MCP)3940> External tools available via [ToolUniverse](https://github.com/mims-harvard/ToolUniverse) MCP server.41> Falls back to Python `requests` + public REST APIs when MCP is unavailable.4243| Source | Tool | Description |44|--------|------|-------------|45| RCSB PDB | `RCSB_search` | RCSB PDB API |46| RCSB PDB | `RCSB_get_structure` | RCSB PDB API |47| UniProt | `UniProt_get_entry` | UniProt API |4849## Quality Gates5051- [ ] The selected method matches the scientific question and stated assumptions.52- [ ] Outputs are reproducible, saved to files, and traceable from inputs to conclusions.53- [ ] Missing data, uncertainty, bias, and hard limits are made explicit.54- [ ] `report.md` and `logs/process-log.jsonl` reference the generated artifacts.55- [ ] No essential result remains chat-only.5657If any gate fails: identify the specific failing check, fix the issue, and re-validate before proceeding.5859## Gotchas6061- PDB structures may contain missing residues or alternate conformations. Check structure completeness before analysis62- Docking scores are relative, not absolute binding affinities. Use for ranking, not predicting Kd values63- Protein identifiers differ across databases (UniProt, PDB, RefSeq). Map to a canonical namespace before integration6465## Validation Loop66671. Execute analysis and generate outputs682. Check:69 - Method selection matches the research question and stated assumptions70 - All outputs are saved to files (no chat-only results)71 - Limitations and uncertainty are explicitly stated72 - `logs/process-log.jsonl` is updated with execution trace733. If any check fails:74 - Identify the failing gate75 - Fix the specific issue76 - Re-run validation774. Proceed only after all gates pass
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