Skill · em Dados, IA e pesquisa

diffdock

Diffusion-based molecular docking. Predict protein-ligand binding poses from PDB/SMILES, confidence scores, virtual screening, for structure-based drug design. Not for affinity prediction.

Procedência

Origem: davila7/claude-code-templates
Caminho: cli-tool/components/skills/scientific/diffdock
Versão fixada: 57f899e5394bb8ca166f38eacae8f0853cbfe033
Licença: MIT
Espelhado em 25/09/2026
nenhum download no Claude Code Templates (lido em 25/09/2026)

Antes de instalar

9 arquivos · 67,3 KB · inclui 3 scripts que executam: scripts/analyze_results.py, scripts/prepare_batch_csv.py, scripts/setup_check.py

Instalar na sua CLI

O comando baixa a versão fixada (commit 57f899e) direto da origem, para a pasta que a CLI lê. Precisa de curl (macOS e Linux); no Windows não há comando, porque o Rook Labs é para macOS.

Claude Code

Neste projeto: instala em .claude/skills/diffdock/.

d=".claude/skills/diffdock"
u="https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/cli-tool/components/skills/scientific/diffdock"
curl -fsSL --create-dirs \
  -o "$d/SKILL.md" "$u/SKILL.md" \
  -o "$d/assets/batch_template.csv" "$u/assets/batch_template.csv" \
  -o "$d/assets/custom_inference_config.yaml" "$u/assets/custom_inference_config.yaml" \
  -o "$d/references/confidence_and_limitations.md" "$u/references/confidence_and_limitations.md" \
  -o "$d/references/parameters_reference.md" "$u/references/parameters_reference.md" \
  -o "$d/references/workflows_examples.md" "$u/references/workflows_examples.md" \
  -o "$d/scripts/analyze_results.py" "$u/scripts/analyze_results.py" \
  -o "$d/scripts/prepare_batch_csv.py" "$u/scripts/prepare_batch_csv.py" \
  -o "$d/scripts/setup_check.py" "$u/scripts/setup_check.py" \
  -o "$d/LICENSE" "https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/LICENSE"

Global: instala em ~/.claude/skills/diffdock/.

d="$HOME/.claude/skills/diffdock"
u="https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/cli-tool/components/skills/scientific/diffdock"
curl -fsSL --create-dirs \
  -o "$d/SKILL.md" "$u/SKILL.md" \
  -o "$d/assets/batch_template.csv" "$u/assets/batch_template.csv" \
  -o "$d/assets/custom_inference_config.yaml" "$u/assets/custom_inference_config.yaml" \
  -o "$d/references/confidence_and_limitations.md" "$u/references/confidence_and_limitations.md" \
  -o "$d/references/parameters_reference.md" "$u/references/parameters_reference.md" \
  -o "$d/references/workflows_examples.md" "$u/references/workflows_examples.md" \
  -o "$d/scripts/analyze_results.py" "$u/scripts/analyze_results.py" \
  -o "$d/scripts/prepare_batch_csv.py" "$u/scripts/prepare_batch_csv.py" \
  -o "$d/scripts/setup_check.py" "$u/scripts/setup_check.py" \
  -o "$d/LICENSE" "https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/LICENSE"

Codex

Neste projeto: instala em .agents/skills/diffdock/.

d=".agents/skills/diffdock"
u="https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/cli-tool/components/skills/scientific/diffdock"
curl -fsSL --create-dirs \
  -o "$d/SKILL.md" "$u/SKILL.md" \
  -o "$d/assets/batch_template.csv" "$u/assets/batch_template.csv" \
  -o "$d/assets/custom_inference_config.yaml" "$u/assets/custom_inference_config.yaml" \
  -o "$d/references/confidence_and_limitations.md" "$u/references/confidence_and_limitations.md" \
  -o "$d/references/parameters_reference.md" "$u/references/parameters_reference.md" \
  -o "$d/references/workflows_examples.md" "$u/references/workflows_examples.md" \
  -o "$d/scripts/analyze_results.py" "$u/scripts/analyze_results.py" \
  -o "$d/scripts/prepare_batch_csv.py" "$u/scripts/prepare_batch_csv.py" \
  -o "$d/scripts/setup_check.py" "$u/scripts/setup_check.py" \
  -o "$d/LICENSE" "https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/LICENSE"

Global: instala em ~/.agents/skills/diffdock/.

d="$HOME/.agents/skills/diffdock"
u="https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/cli-tool/components/skills/scientific/diffdock"
curl -fsSL --create-dirs \
  -o "$d/SKILL.md" "$u/SKILL.md" \
  -o "$d/assets/batch_template.csv" "$u/assets/batch_template.csv" \
  -o "$d/assets/custom_inference_config.yaml" "$u/assets/custom_inference_config.yaml" \
  -o "$d/references/confidence_and_limitations.md" "$u/references/confidence_and_limitations.md" \
  -o "$d/references/parameters_reference.md" "$u/references/parameters_reference.md" \
  -o "$d/references/workflows_examples.md" "$u/references/workflows_examples.md" \
  -o "$d/scripts/analyze_results.py" "$u/scripts/analyze_results.py" \
  -o "$d/scripts/prepare_batch_csv.py" "$u/scripts/prepare_batch_csv.py" \
  -o "$d/scripts/setup_check.py" "$u/scripts/setup_check.py" \
  -o "$d/LICENSE" "https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/LICENSE"

Antigravity

Neste projeto: instala em .agents/skills/diffdock/.

d=".agents/skills/diffdock"
u="https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/cli-tool/components/skills/scientific/diffdock"
curl -fsSL --create-dirs \
  -o "$d/SKILL.md" "$u/SKILL.md" \
  -o "$d/assets/batch_template.csv" "$u/assets/batch_template.csv" \
  -o "$d/assets/custom_inference_config.yaml" "$u/assets/custom_inference_config.yaml" \
  -o "$d/references/confidence_and_limitations.md" "$u/references/confidence_and_limitations.md" \
  -o "$d/references/parameters_reference.md" "$u/references/parameters_reference.md" \
  -o "$d/references/workflows_examples.md" "$u/references/workflows_examples.md" \
  -o "$d/scripts/analyze_results.py" "$u/scripts/analyze_results.py" \
  -o "$d/scripts/prepare_batch_csv.py" "$u/scripts/prepare_batch_csv.py" \
  -o "$d/scripts/setup_check.py" "$u/scripts/setup_check.py" \
  -o "$d/LICENSE" "https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/LICENSE"

Global: instala em ~/.gemini/antigravity-cli/skills/diffdock/.

d="$HOME/.gemini/antigravity-cli/skills/diffdock"
u="https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/cli-tool/components/skills/scientific/diffdock"
curl -fsSL --create-dirs \
  -o "$d/SKILL.md" "$u/SKILL.md" \
  -o "$d/assets/batch_template.csv" "$u/assets/batch_template.csv" \
  -o "$d/assets/custom_inference_config.yaml" "$u/assets/custom_inference_config.yaml" \
  -o "$d/references/confidence_and_limitations.md" "$u/references/confidence_and_limitations.md" \
  -o "$d/references/parameters_reference.md" "$u/references/parameters_reference.md" \
  -o "$d/references/workflows_examples.md" "$u/references/workflows_examples.md" \
  -o "$d/scripts/analyze_results.py" "$u/scripts/analyze_results.py" \
  -o "$d/scripts/prepare_batch_csv.py" "$u/scripts/prepare_batch_csv.py" \
  -o "$d/scripts/setup_check.py" "$u/scripts/setup_check.py" \
  -o "$d/LICENSE" "https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/LICENSE"

Peça ao Rook

Já usa o Rook Labs? Cole no chat do Rook: instale a skill https://rooklabs.sh/marketplace/cct.diffdock

Prévia do SKILL.md

---
name: diffdock
description: "Diffusion-based molecular docking. Predict protein-ligand binding poses from PDB/SMILES, confidence scores, virtual screening, for structure-based drug design. Not for affinity prediction."
---

# DiffDock: Molecular Docking with Diffusion Models

## Overview

DiffDock is a diffusion-based deep learning tool for molecular docking that predicts 3D binding poses of small molecule ligands to protein targets. It represents the state-of-the-art in computational docking, crucial for structure-based drug discovery and chemical biology.

**Core Capabilities:**
- Predict ligand binding poses with high accuracy using deep learning
- Support protein structures (PDB files) or sequences (via ESMFold)
- Process single complexes or batch virtual screening campaigns
- Generate confidence scores to assess prediction reliability
- Handle diverse ligand inputs (SMILES, SDF, MOL2)

**Key Distinction:** DiffDock predicts **binding poses** (3D structure) and **confidence** (prediction certainty), NOT binding affinity (ΔG, Kd). Always combine with scoring functions (GNINA, MM/GBSA) for affinity assessment.

## When to Use This Skill

This skill should be used when:

- "Dock this ligand to a protein" or "predict binding pose"
- "Run molecular docking" or "perform protein-ligand docking"
- "Virtual screening" or "screen compound library"
- "Where does this molecule bind?" or "predict binding site"
- Structure-based drug design or lead optimization tasks
- Tasks involving PDB files + SMILES strings or ligand structures
- Batch docking of multiple protein-ligand pairs

## Installation and Environment Setup

### Check Environment Status

Before proceeding with DiffDock tasks, verify the environment setup:

```bash
# Use the provided setup checker
…

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