binding-affinity

Hybrid ML + physics binding affinity prediction. Empirical scoring, MM/GBSA rescoring, multi-method consensus, and batch virtual screening for protein-ligand complexes.

Quality

66%

Does it follow best practices?

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Securityby

Passed

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tessl review fix ./backend/cli/skills/chemistry/binding-affinity/SKILL.md

Quality

Content

65%

Reviews the quality of instructions and guidance provided to agents. Good implementation is clear, handles edge cases, and produces reliable results.

The content is highly actionable with concrete, executable workflows and real script references, but it is somewhat verbose and keeps detailed reference material inline rather than distributing it to bundled files.

Suggestions

Move the detailed output-format JSON, pKd/Kd interpretation tables, and academic citations into references/ and link them one level deep from the body.

Add explicit validation/feedback checkpoints (e.g. verify output JSON parses, check confidence flags before ranking) to the batch and rescoring workflows.

Trim repeated caveats about computational-estimate uncertainty that appear in both the Validation Warning and Output Interpretation sections.

Dimension	Reasoning	Score
Conciseness	Mostly efficient and well-organized, but restates concepts Claude already knows (pKd/Kd interpretation tables, MM/GBSA caveats) across multiple sections and includes an academic citation list, so it could be tightened.	2 / 3
Actionability	Provides fully executable commands with concrete flags, real script paths, and worked JSON output examples that are copy-paste ready.	3 / 3
Workflow Clarity	Multi-step workflows are clearly sequenced (including a numbered full pipeline), but batch and rescoring operations lack explicit validate->fix->retry feedback loops, which caps clarity at 2.	2 / 3
Progressive Disclosure	The body is fairly monolithic: inline JSON output formats, interpretation tables, and academic citations could be offloaded, and the existing references/scoring_methods.md is never linked from the body, so references are not clearly signaled.	2 / 3
	Total	9 / 12 Passed

Description

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.

The description is specific and well-scoped with multiple concrete capabilities and a distinct niche, but it lacks an explicit 'Use when...' trigger clause and misses several natural user phrasings.

Suggestions

Add an explicit 'Use when...' clause naming common trigger phrases such as 'predict binding affinity', 'estimate Kd', 'rescore with MM/GBSA', or 'rank compounds by affinity'.

Include more natural user-facing terms (e.g. 'predict Kd', 'score binding strength', 'estimate binding') alongside the technical keywords.

Dimension	Reasoning	Score
Specificity	Lists multiple concrete actions ('Empirical scoring', 'MM/GBSA rescoring', 'multi-method consensus', 'batch virtual screening') rather than vague language.	3 / 3
Completeness	Clearly answers what the skill does but has no 'Use when...' clause, so the when is only implied; per guidelines this caps completeness at 2.	2 / 3
Trigger Term Quality	Contains relevant domain keywords ('binding affinity', 'MM/GBSA', 'virtual screening') but omits common natural phrasings a user would say like 'predict Kd' or 'score binding strength'.	2 / 3
Distinctiveness Conflict Risk	Targets a clear niche (binding affinity for protein-ligand complexes) with distinct triggers, making conflict with sibling skills unlikely.	3 / 3
	Total	10 / 12 Passed

Validation

87%

Warnings & errors only

Checks the skill against the spec for correct structure and formatting. All validation checks must pass before discovery and implementation can be scored.

Validation — 14 / 16 Passed

Validation for skill structure

Criteria	Description	Result
metadata_version	'metadata.version' is missing	Warning
frontmatter_unknown_keys	Unknown frontmatter key(s) found; consider removing or moving to metadata	Warning

	Total	14 / 16 Passed

Repository: synthetic-sciences/openscience
Path: backend/cli/skills/chemistry/binding-affinity/SKILL.md
Commit: 52845c3

Reviewed: about 11 hours ago

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