A molecular docking tool that predicts how a small molecule may fit into a protein structure. It uses protein structures in PDB format and molecules described by SMILES, and provides pose confidence scores.

Use it to predict binding poses and confidence scores, or to screen many candidate molecules in structure-based drug-design work.

It helps explore possible protein–molecule binding arrangements before laboratory testing, without treating the result as a binding-strength prediction.

diffdock — Skill by jimmc414

Install

Getting it into your agent

One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.

agentmods

npx agentmods add skills/jimmc414/kosmos/diffdock

Any agent

npx skills add jimmc414/Kosmos --skill diffdock

Clone the repo

git clone --depth 1 https://github.com/jimmc414/Kosmos

Made for: Claude Code, Codex.

Per session 40 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.

When invoked 3,601 The whole file, excluding the scripts and references it only reads on demand.

Security scan A 0 findings. Scan, not verified.

Origin unknown No closer match found in the catalogue.

Token cost

What it costs to keep this loaded

Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.

Model	Per session	Once invoked
Fable 5	$0.00040	$0.03601
Opus 5	$0.00020	$0.01801
Sonnet 5	$0.00008	$0.00720
Haiku 4.5	$0.00004	$0.00360

Measured 2d ago against content hash 0a256757c23f, method: parsed. Prices are Anthropic first-party input rates as of 2026-08-30, from the pricing page.

Security

Grade A, and why

diffdock scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 2d ago.

The scan reads SKILL.md. This mod also ships 3 executable files (scripts/analyze_results.py, scripts/prepare_batch_csv.py, scripts/setup_check.py), listed below but not scanned — reading those needs a real analyzer, not pattern matching.

A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.

Nothing flagged

None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.

kosmos-claude-scientific-skills/scientific-skills/diffdock/SKILL.md · 478 lines

The source is not reproduced here

No licence file

Read it on GitHub

Files

What ships with it

8 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.

Changes

What this file has done since we first saw it

Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.

2d ago First seen · 478 lines · 40 tokens per session scan A 0a256757c23f

Subscribe to this mod's changes

diffdock is a skill published in the GitHub repository jimmc414/Kosmos (576 stars, last pushed 5mo ago), with no licence file. It adds 40 tokens to every session and 3,601 once invoked, about $0.0002 per session on Opus 5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-30.

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