Build

diffdock

by open-science

Predict small-molecule binding poses with DiffDock-L (Corso et al. 2023/2024, github.com/gcorso/DiffDock) — blind diffusion docking that places a ligand into a protein pocket without a predefined search box and ranks the samples with a learned confidence model. Reach for this skill to dock a SMILES or SDF against a PDB, to generate ranked 3D poses for a small fragment library, or to get a starting pose for downstream rescoring. DiffDock predicts geometry, not affinity.

v1.0.0New

Unsigned, install at your own risk

Unverified

This skill has no cryptographic signature attached. We can't verify the contents match what the publisher intended.

Install this skill

Run this command in your terminal. No account required — it auto-detects your AI tool and installs the skill file.

npx @skills-hub-ai/cli install open-science-diffdock
Or download directly:
Browse all CLI commands →

Setup by platform

Claude Code

~/.claude/skills/<skill>/SKILL.md

Setup guide →

Install

One-click setup for your editor

Run in your project root

npx @skills-hub-ai/cli install open-science-diffdock --target claude-code
0

Instructions

This skill doesn’t include stateful context yet, instructions only. Learn about stateful skills.

Security

Loading security scan...

Reviews (0)

View full changelog & diffs →

Related skills

Browse all →
remote-compute-sshEvaluate and use SSH Remote Compute before choosing where to run GPU, high-memory, parallel, batch, model-inference, bioinformatics, or other long-running scientific work; supports short remote commands and asynchronous jobs with automatic harvest and analysis.0 installsskill-creatorCreate, revise, evaluate, publish, and improve Open-Science Skills through the native JavaScript host.skills composer. Use when the user wants a reusable workflow, an existing Skill changed, test cases or benchmarks for a Skill, or better Skill triggering.0 installsproteinmpnnInverse-fold a protein backbone (PDB structure) into amino-acid sequence with ProteinMPNN (Dauparas et al. 2022, github.com/dauparas/ProteinMPNN). Reach for this skill to run sequence design on RFdiffusion backbones, to redesign one chain of a PDB while holding interface residues fixed, or to generate a temperature-swept set of sequences for downstream folding.0 installssolublempnnInverse-fold a backbone with SolubleMPNN — ProteinMPNN retrained on a soluble-PDB subset (Dauparas et al. 2022) — for sequences biased toward cytosolic expression and reduced aggregation. Reach for this skill when designs from vanilla ProteinMPNN are aggregating or going to inclusion bodies, when redesigning a membrane-adjacent fold for soluble expression, or when an E. coli expression screen is the next step.0 installsalphafold2Predict protein structure for monomers and multimers with AlphaFold2 via the ColabFold runner (Mirdita et al. 2022, github.com/sokrypton/ColabFold; AlphaFold2 Jumper et al. 2021). Reach for this skill to fold a sequence or complex with the AF2/AF2-Multimer evoformer, to validate designed sequences by self-consistency pLDDT, ipTM, and RMSD, or to run a quick MSA-backed prediction using the public MMseqs2 server.0 installsindication-dossierGenerate a therapeutic indication dossier. Covers the patient population, epidemiology, disease biology, standard of care, regulatory precedent, and landmark clinical trials.0 installs

More from open-science

View source →
compute-env-setupPrepare reproducible setup instructions and validate a user-managed named software environment on an Open-Science SSH Compute Host, including direct SSH and Slurm hosts. Use when a remote job needs packages, modules, cache variables, or a repeatable activation that the host does not already provide.0 installsesmfold2Biohub ESMFold2 / ESMFold2-Fast all-atom co-folding (Candido et al. 2026, github.com/Biohub/esm). Single-sequence and MSA modes; protein, DNA, RNA, ligand (CCD/SMILES), modified residues. FoldBench Ab-Ag 50-55%, PPI 70-77% DockQ-pass. Also covers the ESMC-{300M,600M,6B} protein language models from the same release: masked-LM logits, hidden states, mutation scoring, contact prediction, and the SAE interpretability head. MIT-licensed weights on HuggingFace org `biohub`. Use this skill when: (1) Predicting complex structures with single-sequence input, (2) Validating designed binders with ESMFold2-Fast, (3) Running ESMFold2 with MSA input, (4) Getting ESMC embeddings or per-residue mutation scores, (5) Choosing kernel backend and sampling-step settings for paper-faithful throughput.0 installsfair-esm2Embed proteins with Meta AI's ESM-2 (`fair-esm` package). Use this skill when: (1) Extracting per-residue or per-sequence embeddings for downstream ML, (2) Masked-LM likelihood / mutation effect scoring, (3) Contact prediction from a sequence.0 installsfigure-stylePublication-grade correctness and legibility rules for final-deliverable scientific figures, not exploratory plots. Use for a figure that will ship in a report, paper, export, or kept artifact. Covers data fidelity, label economy, color threading, chart choice, layout, and render-then-verify QA without imposing a visual house style. For multi-panel composition use `figure-composer`; for whole-paper ordering use `paper-narrative`.0 installsliterature-reviewFind, verify, and synthesize scientific literature — from "what's the seminal paper for X" through full multi-source reviews. Covers grounding claims in real retrieved sources, avoiding fabricated citations, handling retractions, and calibrating confidence to evidence strength.0 installsboltzStructure prediction for protein, nucleic-acid, and small-molecule complexes with Boltz-2 (Passaro & Wohlwend et al. 2025, github.com/jwohlwend/boltz). Reach for this skill to validate designed binders against a target, to co-fold a protein with a SMILES or CCD ligand, or to get an open-source AlphaFold3 alternative with optional binding-affinity prediction.0 installs

More Build skills

Browse category →
ui-design-systemUI design system toolkit for Senior UI Designer including design token generation, component documentation, responsive design calculations, and developer handoff tools. Use when creating design systems, generating design tokens, maintaining visual consistency, or facilitating design-dev collaboration and developer handoff.257 installssenior-frontendFrontend development skill for React, Next.js, TypeScript, and Tailwind CSS applications. Use when building React components, optimizing Next.js performance, analyzing bundle sizes, scaffolding frontend projects, implementing accessibility, or reviewing frontend code quality.192 installsfrontend-designGuidance for distinctive, intentional visual design when building new UI or reshaping an existing one. Helps with aesthetic direction, typography, and making choices that don't read as templated defaults.139 installsself-improving-agentCurate Claude Code's auto-memory into durable project knowledge. Analyze MEMORY.md for patterns, promote proven learnings to CLAUDE.md and .claude/rules/, extract recurring solutions into reusable skills. Use when: (1) reviewing what Claude has learned about your project, (2) graduating a pattern from notes to enforced rules, (3) turning a debugging solution into a skill, (4) checking memory health and capacity.95 installssenior-backendDesigns and implements backend systems including REST APIs, microservices, database architectures, authentication flows, and security hardening. Use when the user asks to "design REST APIs", "optimize database queries", "implement authentication", "build microservices", "review backend code", "set up GraphQL", "handle database migrations", or "load test APIs". Covers Node.js/Express/Fastify development, PostgreSQL optimization, API security, and backend architecture patterns.87 installsusing-superpowersUse when starting any conversation - establishes how to find and use skills, requiring skill invocation before ANY response including clarifying questions73 installs

Frequently asked questions about diffdock

What does the diffdock skill do?

Predict small-molecule binding poses with DiffDock-L (Corso et al. 2023/2024, github.com/gcorso/DiffDock) — blind diffusion docking that places a ligand into a protein pocket without a predefined search box and ranks the samples with a learned confidence model. Reach for this skill to dock a SMILES or SDF against a PDB, to generate ranked 3D poses for a small fragment library, or to get a starting pose for downstream rescoring. DiffDock predicts geometry, not affinity. It's a reusable SKILL.md instruction set that loads into your AI coding assistant on demand, no prompt engineering, no copy-pasting every session.

How do I install the diffdock skill?

Run `npx @skills-hub-ai/cli install open-science-diffdock` from your terminal. The CLI writes the SKILL.md to the correct location for your AI tool (e.g. ~/.claude/skills/open-science-diffdock/ for Claude Code or ~/.cursor/skills/ for Cursor with --target cursor) and adds it to your project's .skills.json lockfile.

Which AI tools does diffdock work with?

diffdock runs in Claude Code. It follows the open Agent Skills standard (SKILL.md), so the same skill works in every supported tool without modification.

Is the diffdock skill free?

Yes. Every skill on skills-hub.ai is free and open-source. There are no premium tiers, paywalls, or usage limits. You only pay for whatever AI assistant you're already using.

How do I use diffdock after installing it?

In Claude Code, type `/open-science-diffdock` (or whatever slash command the skill registers) and the AI follows the skill's instructions immediately. You can also reference it by name in natural language, your AI loads the skill into context when relevant.

Can I share the diffdock skill with my team?

Yes. Commit your project's .skills.json lockfile and teammates run `npx @skills-hub-ai/cli install` (no args) to install every skill at the exact version you pinned. Organization-scoped installs work via skills-hub.ai organizations.