diffdock

diffdock is a skill for Claude Code, Codex from MarieLynneBlock/arcanum-artifex. It costs 40 tokens per session (3,619 once invoked), scanned A, original, no licence file.

A molecular docking tool that predicts how a small molecule may fit into a protein. It uses protein structures in PDB format and molecules written as SMILES, and reports confidence scores.

In plain words
What is it for?
Use it for structure-based drug design and virtual screening of compounds against protein targets.
Why use it?
It helps researchers examine possible protein–drug binding poses before laboratory testing. It does not predict binding strength.

Skill for Claude CodeCodex

Which agent this was written for is unclear — body not stored (licence); the path alone says nothing.

Good fit Use it for structure-based drug design and virtual screening of compounds against protein targets.

Compare 6 skills from other repositories ↓
Install with agentmods
npx agentmods add skills/marielynneblock/arcanum-artifex/diffdock
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.

Any agent
npx skills add MarieLynneBlock/arcanum-artifex --skill diffdock
Clone the repo
git clone --depth 1 https://github.com/MarieLynneBlock/arcanum-artifex

Made for: Claude Code, Codex.

Wrote this? Show the measurements

A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.

agentmods badge for diffdock

README.md
[![agentmods](https://agentmods.dev/badge/skills/marielynneblock/arcanum-artifex/diffdock/github.svg)](https://agentmods.dev/skills/marielynneblock/arcanum-artifex/diffdock)
Your own site
<a href="https://agentmods.dev/skills/marielynneblock/arcanum-artifex/diffdock"><img src="https://agentmods.dev/badge/skills/marielynneblock/arcanum-artifex/diffdock/github.svg" alt="Measured on agentmods" height="20"></a>

Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.

agentmods 80×15 button for diffdock

Your own site · 80×15
<a href="https://agentmods.dev/skills/marielynneblock/arcanum-artifex/diffdock"><img src="https://agentmods.dev/badge/skills/marielynneblock/arcanum-artifex/diffdock.svg" alt="Reviewed on agentmods" width="80" height="20"></a>
Per session 40 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.
When invoked 3,619 The whole file, excluding the scripts and references it only reads on demand.
Security scan A 0 findings. A grade says what 26 rules found in the file — not that it is safe.
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.

ModelPer sessionOnce invoked
Fable 5.1 $0.00040 $0.03619
Opus 5 $0.00020 $0.01809
Sonnet 5 $0.00008 $0.00724
Haiku 4.5 $0.00004 $0.00362

Measured 10d ago against content hash fbe5acbf3738, method: parsed. Prices are Anthropic first-party input rates as of 2026-09-13, 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 10d 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.

skills/scientific/diffdock/SKILL.md · 481 lines

The source is not reproduced here

No licence file

A repository with no LICENSE is all rights reserved by default, so the body is not copied here. The metadata, the measurements and the link are.

Read it on GitHub

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.

  1. 10d ago First seen · 481 lines · 40 tokens per session scan A fbe5acbf3738

Subscribe to this mod's changes

diffdock is a skill published in the GitHub repository MarieLynneBlock/arcanum-artifex (4 stars, last pushed 8d ago), with no licence file. It adds 40 tokens to every session and 3,619 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 2026-09-03.