protein-docking-configurator
Prepare input files for molecular docking software, automatically determine Grid Box center and size. Supports AutoDock Vina, AutoDock4, and other mainstream docking tools.
Install with Tessl CLI
npx tessl i github:aipoch/medical-research-skills --skill protein-docking-configurator72
Does it follow best practices?
If you maintain this skill, you can automatically optimize it using the tessl CLI to improve its score:
npx tessl skill review --optimize ./path/to/skillValidation for skill structure
Discovery
67%Based on the skill's description, can an agent find and select it at the right time? Clear, specific descriptions lead to better discovery.
This is a technically specific description that clearly identifies its domain (molecular docking) and lists concrete capabilities. However, it lacks an explicit 'Use when...' clause which would help Claude know exactly when to select this skill. The trigger terms are adequate but could include more user-friendly variations.
Suggestions
Add a 'Use when...' clause with trigger terms like 'docking simulation', 'ligand binding', 'protein-ligand docking', 'PDBQT files'
Include common user phrases such as 'prepare docking files', 'set up AutoDock', or 'virtual screening preparation'
| Dimension | Reasoning | Score |
|---|---|---|
Specificity | Lists multiple specific concrete actions: 'Prepare input files', 'determine Grid Box center and size', and names specific tools (AutoDock Vina, AutoDock4). These are concrete, domain-specific capabilities. | 3 / 3 |
Completeness | Clearly answers 'what' (prepare input files, determine grid box parameters, supports specific tools) but lacks an explicit 'Use when...' clause or equivalent trigger guidance. The 'when' is only implied by the domain context. | 2 / 3 |
Trigger Term Quality | Includes relevant technical terms like 'molecular docking', 'AutoDock Vina', 'AutoDock4', 'Grid Box', but missing common user variations like 'ligand docking', 'protein-ligand', 'PDBQT', or simpler terms users might say like 'docking simulation'. | 2 / 3 |
Distinctiveness Conflict Risk | Highly specialized niche in computational chemistry/bioinformatics. Terms like 'molecular docking', 'Grid Box', 'AutoDock Vina' are very specific and unlikely to conflict with other skills. | 3 / 3 |
Total | 10 / 12 Passed |
Implementation
64%Reviews the quality of instructions and guidance provided to agents. Good implementation is clear, handles edge cases, and produces reliable results.
This skill provides solid, actionable guidance for configuring molecular docking software with executable examples and comprehensive parameter documentation. However, it's bloated with boilerplate sections (Risk Assessment, Security Checklist, Evaluation Criteria, Lifecycle Status) that don't help Claude perform the task, and it lacks validation steps to verify output correctness before proceeding to docking.
Suggestions
Remove or relocate boilerplate sections (Risk Assessment, Security Checklist, Evaluation Criteria, Lifecycle Status) that don't provide actionable guidance
Add validation steps to verify generated Grid Box parameters are reasonable (e.g., check box dimensions, visualize box placement, validate output file format)
Include a brief workflow showing the complete process: prepare receptor → generate config → validate config → run docking, with checkpoints at each stage
| Dimension | Reasoning | Score |
|---|---|---|
Conciseness | The skill includes useful content but has unnecessary sections like Risk Assessment, Security Checklist, Evaluation Criteria, and Lifecycle Status that add bulk without providing actionable guidance for Claude. The core technical content is reasonably efficient. | 2 / 3 |
Actionability | Provides fully executable command-line examples and Python code snippets that are copy-paste ready. The parameter table is comprehensive, and multiple concrete examples demonstrate different use cases with specific file names and arguments. | 3 / 3 |
Workflow Clarity | The skill shows how to use the tool but lacks validation checkpoints. There's no guidance on verifying output correctness, handling errors, or confirming the generated Grid Box is appropriate before proceeding to docking. The Notes section hints at prerequisites but doesn't integrate them into a workflow. | 2 / 3 |
Progressive Disclosure | Content is reasonably organized with clear sections, but everything is in one file with no references to external documentation. The parameter table and examples could be split out for a cleaner overview. The boilerplate sections (Risk Assessment, Security Checklist, etc.) clutter the main content. | 2 / 3 |
Total | 9 / 12 Passed |
Validation
90%Checks the skill against the spec for correct structure and formatting. All validation checks must pass before discovery and implementation can be scored.
Validation — 10 / 11 Passed
Validation for skill structure
| Criteria | Description | Result |
|---|---|---|
frontmatter_unknown_keys | Unknown frontmatter key(s) found; consider removing or moving to metadata | Warning |
Total | 10 / 11 Passed | |
- Reviewed
Table of Contents
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