Anyone can dock, everyone can do!

Anyone docking: Browser-based molecular docking — no installation required.

Paste a SMILES, draw a structure, or upload a file. Pick a PDB or CIF. Dock in seconds.

Recent updates: New CLI and Python API via anyonecandock on PyPI. New redock command — automatically re-docks the co-crystal ligand with zero SMILES input (RCSB CCD lookup → CIF block → 3D fallback). Receptor setup now auto-scans ligand-like HETATM records. Ligand preparation supports pKaNET-ranked microstates with manual rank selection.

🚀 Six ways to use Anyone Can Dock

Mode	Best for	How
🌐 Streamlit Web App	Quickest start, no setup	Open in browser →
☁️ Streamlit via Colab	Web UI on free GPU/CPU
🖥️ Streamlit locally	Full control, own machine	`pip install anyonecandock && streamlit run app.py`
📓 Colab notebook	Batch docking, scripting
⌨️ CLI (`acd`)	Automation, pipelines, scripts	`pip install anyonecandock` then `acd dock ...`
🐍 Python API	Programmatic integration	`from anyonecandock import core`
🤖 GPT / Claude plugin	Natural-language docking	See below ↓

🤖 AI Interfaces

Anyone Can Dock GPT

Ask GPT-4o to dock molecules using natural language.

Anyone Can Dock in Claude

Connect Claude to the ACD API as a custom MCP connector — ask Claude to dock molecules, search PDB targets, and interpret results directly in the chat.

Setup (3 steps):

Copy the MCP server URL:

https://anyone-can-dock-mcp.anyonecandock.workers.dev

Click the badge below to open Claude Connectors settings, then click "Add custom connector"
Paste the URL into Remote MCP server URL and click Add

Example prompts after connecting:

"dock quercetin into JAK2 and report binding affinity"
"compare erlotinib vs gefitinib binding to EGFR (1M17)"

Powered by: AutoDock Vina 1.2.7 · pKaNET protonation at pH 7.4 · MCP Streamable HTTP

MCP server URL: https://anyone-can-dock-mcp.anyonecandock.workers.dev

⌨️ CLI — `acd` command

Install from PyPI:

pip install anyonecandock

Commands

acd <command> [options]

  dock      Full pipeline: receptor + ligand + Vina (single ligand)
  redock    Self-docking validation — no SMILES input needed
  batch     Batch docking from a .smi file or SMILES list
  receptor  Prepare receptor only (download/convert → .pdb + .pdbqt + box)
  ligand    Prepare ligand only (SMILES/file → .pdbqt + .sdf)
  diagram   Generate a 2D interaction diagram SVG for a completed run

Quick examples

# Dock a single ligand by compound name
acd dock --receptor 1M17 --compound erlotinib

# Dock by SMILES
acd dock --receptor 4AGN --smiles "CCO" --name ethanol

# Dock from an existing receptor preparation (skips re-prep)
acd dock --receptor-json ./rec/receptor_summary.json --compound baicalein

# Dock from a structure file
acd dock --receptor structure.cif --ligand-file ligand.sdf --name mylig

# ── Redocking (self-docking validation) — NEW ──────────────────────────
# Re-docks the co-crystal ligand automatically; no SMILES required.
# SMILES acquired via: RCSB CCD → CIF _chem_comp.pdbx_smiles → 3D fallback
acd redock --receptor 4AGN
acd redock --receptor structure.cif --fmt CIF
acd redock --receptor 4AGN --resname DC3 --diagram
acd redock --receptor-json ./rec/receptor_summary.json

# Batch docking
acd batch --receptor 1M17 --ligands compounds.smi
acd batch --receptor 4AGN --smiles-list "CCO ethanol" "c1ccccc1O phenol"

`acd redock` — self-docking validation

The redock command automatically identifies and re-docks the co-crystal ligand present in a PDB/CIF structure — no SMILES input required.

acd redock --receptor <PDB_ID_or_FILE> [options]

Options:
  --resname     Override the auto-detected ligand residue name (e.g. DC3, ATP)
  --name        Output name for the re-docked ligand (default: residue code)
  --ph          Target pH for protonation (default: 7.4)
  --diagram     Generate 2D interaction diagram after docking
  --save-poses  Save each docked pose as an individual SDF/PDB file
  -e / --exhaustiveness   Vina exhaustiveness (default: 16)
  -n / --poses            Max poses to output (default: 10)
  -o / --output           Output directory (default: ./acd_redock)

SMILES acquisition order:

RCSB CCD REST API — ideal, stereo-correct, curated SMILES from the PDB chemical component dictionary
CIF _chem_comp.pdbx_smiles — parsed directly from the structure CIF (no network required)
3D coordinate conversion — RDKit + OpenBabel with hydrogen-aware bond perception (last resort; a warning is shown)

Redocking verdict (printed automatically):

✓ PASS — best pose RMSD ≤ 2.0 Å vs crystal
⚠ BORDERLINE — RMSD 2–3 Å
✗ FAIL — RMSD > 3.0 Å

All `acd dock` options

usage: acd dock [options]
acd dock --help

Protein:
  --receptor PDB_ID_or_FILE
      PDB ID (auto-downloaded) or path to .pdb/.cif
  --receptor-json PATH
      JSON from a previous acd receptor run
  --fmt {PDB,CIF}
      Input format (default: PDB)

Ligand:
  --smiles SMILES
      Ligand SMILES string
  --compound NAME
      Compound name for PubChem lookup
  --ligand-file PATH
      Ligand structure file (.sdf/.mol2/.pdb)
  --name NAME
      Output name (default: LIG)
  --ph PH
      Target pH (default: 7.4)
  --neutral
      Keep the input charge and add hydrogens only
  --no-pubchem
      Skip PubChem pKa lookup

Docking box:
  --center {auto,manual,selection}
      Box center mode (default: auto)
  --cx X
      Manual box-center X coordinate
  --cy Y
      Manual box-center Y coordinate
  --cz Z
      Manual box-center Z coordinate
  --bx Å
      Box X size, 10–40 Å (default: 18)
  --by Å
      Box Y size, 10–40 Å (default: 18)
  --bz Å
      Box Z size, 10–40 Å (default: 18)

pKaNET:
  --max-tautomers N
      Maximum tautomers, 1–20 (default: 8)
  --ph-window PH
      pH window, 0.2–2.0 (default: 1.0)
  --conformer-seed N
      RDKit conformer seed (default: random)

Vina:
  -e N, --exhaustiveness N
      Vina exhaustiveness (default: 16)
  -n N, --poses N
      Maximum poses (default: 10)
  --energy-range KCAL
      Energy range in kcal/mol (default: 3)
  --seed N
      Vina random seed (default: random)

Validation and output:
  --redock-smiles "SMILES [name]"
      Dock a reference co-crystal ligand
  --save-poses
      Save individual pose files
  --diagram
      Generate a 2D interaction diagram
  -o OUTPUT, --output OUTPUT
      Output directory (default: ./acd_results)

🐍 Python API

from anyonecandock import core

# Reproducibility settings
SEED = 72
BOX_SIZE = (18, 18, 18)
vina_bin = "/path/to/vina"

# Prepare receptor
result = core.prepare_receptor(
    raw_pdb="raw.pdb",
    wdir="./rec",
    box_size=BOX_SIZE,
)

# Prepare ligand using heuristic pKaNET backend
lig = core.prepare_ligand(
    smiles="c1ccc(cc1)O",
    name="phenol",
    ph=7.4,
    wdir="./lig",
    mode="pkanet",
    use_pubchem=False,
    max_tautomers=8,
    ph_window=1.0,
    conformer_seed=SEED,
)

# Run deterministic docking
dock = core.run_vina(
    receptor_pdbqt=result["rec_pdbqt"],
    ligand_pdbqt=lig["pdbqt"],
    config_txt=result["config_txt"],
    vina_path=vina_bin,
    exhaustiveness=16,
    n_modes=10,
    energy_range=3,
    seed=SEED,
    wdir="./out",
    out_name="phenol",
)

print("Top score:", dock["top_score"])

# Auto-detect co-crystal SMILES
smiles, source, warning = core.get_cocrystal_smiles(
    ligand_pdb_path=result["ligand_pdb_path"],
    cocrystal_ligand_id=result["cocrystal_ligand_id"],
    raw_pdb="raw.cif",
)

print(f"SMILES source: {source}")
print(f"SMILES: {smiles}")
if warning:
    print(f"Warning: {warning}")

# 2D interaction diagram
svg_bytes = core.draw_interaction_diagram(
    receptor_pdb=result["rec_fh"],
    pose_sdf="./out/phenol_out.sdf",
    smiles=lig["prot_smiles"],
    title="Phenol · 4AGN",
)

with open("./out/diagram.svg", "wb") as handle:
    handle.write(svg_bytes)

🌐 Streamlit Web App

The simplest entry point — no installation, runs in the browser.

Supports single and batch docking, all 2D diagram engines, interactive drag layout, ADME predictions, and ready-to-use figure export.

☁️ Streamlit via Google Colab

Run the full Streamlit web interface on Colab's free compute tier — no local install needed.

📓 Colab Notebook (batch docking)

Batch docking with 4 docking engines in a Python notebook environment:

🖥️ Run Streamlit locally

The local app uses the deterministic heuristic pKaNET backend. ML pKa backends are disabled.

Linux (Ubuntu/Debian)

sudo apt update

sudo apt install -y \
  python3.11 \
  python3.11-venv \
  openbabel \
  libcairo2-dev \
  libpango1.0-dev \
  libpangocairo-1.0-0

git clone https://github.com/nyelidl/anyone-docking-local.git
cd anyone-docking-local

python3.11 -m venv venv
source venv/bin/activate

python -m pip install --upgrade pip
python -m pip install -r requirements.txt

streamlit run app.py

macOS

brew update
brew install python@3.11 open-babel cairo pango

git clone https://github.com/nyelidl/anyone-docking-local.git
cd anyone-docking-local

python3.11 -m venv venv
source venv/bin/activate

python -m pip install --upgrade pip
python -m pip install -r requirements.txt

streamlit run app.py

Apple Silicon (M1–M4): Fully supported — the app auto-downloads the correct aarch64 Vina binary.

Windows

Recommended: Use WSL2 with Ubuntu and follow the Linux instructions above.

For native Windows:

Install OpenBabel from openbabel.org and add to PATH
Install Cairo/Pango via conda: conda install -c conda-forge cairo pango

git clone https://github.com/nyelidl/anyone-docking-local.git
cd anyone-docking-local
python -m venv venv && venv\Scripts\activate
pip install -r requirements.txt
streamlit run app.py

Streamlit Cloud deployment

anyone-docking/
├── app.py
├── core.py
├── requirements.txt   # Python packages
└── packages.txt       # System packages (openbabel, libcairo2-dev, …)

✨ What it does


🔬	Single & batch docking via AutoDock Vina 1.2.7
♻️	`redock` — self-docking validation — auto-fetches co-crystal SMILES (RCSB CCD → CIF → 3D), docks, reports RMSD verdict
🏗️	Guided receptor prep — download any PDB/CIF, review ligand candidates automatically, strip solvent, add hydrogens
📄	PDB & mmCIF support — upload `.pdb` or `.cif` files or download from RCSB (auto-fallback to CIF for large entries)
🎯	Smart grid detection — auto-detects ligand-like HETATM records; shows dropdown only when multiple candidates exist
✏️	3-way ligand input — SMILES text, file upload, or draw in Ketcher
🧬	pKaNET-ranked microstates — tautomer-aware protonation at target pH with manual rank selection Open in browser →
⚖️	Conservative docking-state selection — avoids over-deprotonated states for polyphenols, flavonoids, coumarins
🧬	Heme-aware preparation — HEM/HEC/HEA/HEB stripped before OpenBabel, re-injected with correct AD4 atom types
⚗️	Water/cofactor/metal control — remove waters, keep metals, keep/strip FAD/NAD/ATP/CoA independently
🗺️	Three 2D diagram engines: ACD custom SVG · RDKit · PoseView (proteins.plus)
🖱️	Interactive drag mode — reposition residue labels in real time, export PNG (up to 600 dpi) or SVG
🔭	Binding pocket viewer — interacting residues as orange sticks with adjustable distance cutoff
🤖	AI-ready prompt — auto-filled for Claude, GPT-4o, Gemini; adapts to redocking context
📊	3D viewers — animated multi-pose sweep, pose selector, binding pocket view
📁	One-click ZIP — all poses, corrected SDFs, diagrams, score plot, pKaNET log

🗺️ 2D Interaction Diagrams

Three tabs — each with a different rendering engine:

🧬 Anyone Can Dock 2D Diagram (default)

Feature	Detail
8 interaction types	H-bond (distance on line), hydrophobic, π-π, cation-π, ionic, metal/heme, halogen bond, H···halogen
Geometry-based	All interactions computed from 3D coordinates — no server, works offline
ACS-style bonds	Bond widths, double-bond spacing, and wedge geometry follow ACS publication standards
Smart layout	Radial placement by interaction angle; push-apart prevents overlap
Interactive drag	Reposition any residue label in real time; distance labels update live
Export	SVG (vector) · PNG at 1× / 2× (150 dpi) / 3× (300 dpi) / 4× (600 dpi)

🔬 RDKit 2D Diagram

Classic highlight-circle style. H-bond (blue) · Hydrophobic (green) · Other/metal (pink). Side-by-side with co-crystal reference when available.

🔬 PoseView (proteins.plus)

REST API submission of receptor + docked pose. PoseView v1 (docked pose) + PoseView2 (co-crystal reference by PDB code + ligand ID). Built-in API test and manual fallback download.

⚠️ PoseView limitation: charged species are shown in neutral form. Use ACD or RDKit diagrams for ligands with formal charges.

🧬 Supported protein types

Protein class	Support	Notes
Standard single-chain proteins	✅ Full	Primary use case
Multi-chain / homo-oligomers	✅ Full	Duplicate chains deduplicated; chain A ligand auto-selected
Heme proteins (CYP450, peroxidases, Hb, Mb)	✅ Full	Fe-porphyrin handled separately; grid auto-centers on Fe
Metal-binding proteins (zinc fingers, carbonic anhydrase)	✅ Full	ZN, MG, CA, MN, FE, CU re-injected with correct charges
MD simulation outputs (GROMACS, AMBER)	✅ Full	Blank chain IDs auto-assigned to chain A
Non-standard ligand names (MOL, LIG, UNL, INH)	✅ Full
Modified amino acids (CYP, MSE, TPO, SEP)	✅ Full	Backbone atom check keeps them in receptor
Multiple co-crystal ligands	✅ Full	Dropdown shown only when needed
Cofactor-binding proteins (FAD, NAD, ATP, CoA)	✅ Full	Kept or stripped independently
Glycoproteins	⚠️ Partial	Glycans kept in receptor; not in 2D diagram
Membrane proteins	⚠️ Partial	Dockable without lipids; lipids not auto-filtered
RNA / DNA targets	⚠️ Partial	Basic interaction detection; no nucleic-acid-specific types
Covalent docking	❌ No	Vina is non-covalent only

♻️ Redocking validation

Available in all modes (Streamlit, CLI acd redock, API, Colab):

Feature	Description
Auto SMILES acquisition	RCSB CCD API → CIF `_chem_comp.pdbx_smiles` → 3D conversion (no manual input needed)
RMSD vs crystal	Heavy-atom RMSD via MCS matching against original crystal pose
Verdict	PASS ≤ 2.0 Å · BORDERLINE 2–3 Å · FAIL > 3.0 Å
Reference score line	Dashed red line on affinity plot
Pose confirmation	Browse reference poses, pin as baseline for score comparisons
Download	Export reference poses as SDF/PDBQT

💻 Platform compatibility

Platform	Vina binary	OpenBabel	Status
Linux x86_64	✅ Auto-download	`apt install openbabel`	Fully supported (primary)
macOS Intel	✅ Auto-download	`brew install open-babel`	Fully supported
macOS Apple Silicon (M1–M4)	✅ Native `aarch64`	`brew install open-babel`	Fully supported
Windows x86_64	✅ Auto-download	Installer	Supported (WSL2 recommended)
Streamlit Cloud	✅ Auto-download	via `packages.txt`	Fully supported
Google Colab	✅ Auto-download	`!apt install openbabel`	Fully supported

🧬 pKaNET microstate selection

Mode	Meaning
Auto recommended	pKaNET recommendation. For ambiguous systems (polyphenols, coumarins, flavonoids), may choose a conservative state rather than the highest score
Highest-scoring	Top-ranked pKaNET state directly
Manual rank	Choose any ranked microstate from a dropdown before docking

⚗️ Water, cofactor & metal options

Option	Default	Effect
Remove waters	✅ On	Removes crystallographic waters
Keep metal ions	✅ On	Keeps ZN, MG, CA, MN, FE, CU, CO, NI, CD, HG, NA, K
Keep cofactors	✅ On	Keeps ATP, ADP, FAD, FMN, NAD, CoA, SAM, HEM

Buffers and additives (GOL, EDO, PEG, SO4, PO4) are removed by default.

📄 Citation

If you use this tool in research, please cite:

AutoDock Vina 1.2.7 Eberhardt et al., J. Chem. Inf. Model., 2021 · DOI: 10.1021/acs.jcim.1c00203

DFDD Hengphasatporn, K.; Duan, L.; Harada, R.; Shigeta, Y., J. Chem. Inf. Model., 2026 · DOI: 10.1021/acs.jcim.5c02852

RDKit · Landrum, G. (2023) · https://www.rdkit.org

ProDy · Bakan et al., Bioinformatics, 2011 · DOI: 10.1093/bioinformatics/btr168

stmol · Nápoles-Duarte et al., Front. Mol. Biosci., 2022 · DOI: 10.3389/fmolb.2022.990846

Dimorphite-DL · Ropp et al., J. Cheminform., 2019 · DOI: 10.1186/s13321-019-0336-9

pKaNET Cloud · Please cite the corresponding manuscript when available.

gemmi (optional, for CIF support) · Wojdyr, M., JOSS, 2022 · DOI: 10.21105/joss.04200

📜 License

MIT License — see LICENSE for details.

Name		Name	Last commit message	Last commit date
Latest commit History 1,097 Commits
.devcontainer		.devcontainer
pKaNET_Cloud_BM		pKaNET_Cloud_BM
st		st
LICENSE		LICENSE
README.md		README.md
Third-Party _Software_License_Declaration.txt		Third-Party _Software_License_Declaration.txt
any-L.svg		any-L.svg
app.py		app.py
core.py		core.py
index.html		index.html
manifest.json		manifest.json
pKaNET.py		pKaNET.py
packages.txt		packages.txt
requirements.txt		requirements.txt

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Anyone can dock, everyone can do!

🚀 Six ways to use Anyone Can Dock

🤖 AI Interfaces

Anyone Can Dock GPT

Anyone Can Dock in Claude

⌨️ CLI — `acd` command

Commands

Quick examples

`acd redock` — self-docking validation

All `acd dock` options

🐍 Python API

🌐 Streamlit Web App

☁️ Streamlit via Google Colab

📓 Colab Notebook (batch docking)

🖥️ Run Streamlit locally

Linux (Ubuntu/Debian)

macOS

Windows

Streamlit Cloud deployment

✨ What it does

🗺️ 2D Interaction Diagrams

🧬 Anyone Can Dock 2D Diagram (default)

🔬 RDKit 2D Diagram

🔬 PoseView (proteins.plus)

🧬 Supported protein types

♻️ Redocking validation

💻 Platform compatibility

🧬 pKaNET microstate selection

⚗️ Water, cofactor & metal options

📄 Citation

📜 License

About

Releases

Packages

Contributors

Languages

Folders and files

Latest commit

History

Repository files navigation

Anyone can dock, everyone can do!

🚀 Six ways to use Anyone Can Dock

🤖 AI Interfaces

Anyone Can Dock GPT

Anyone Can Dock in Claude

⌨️ CLI — acd command

Commands

Quick examples

acd redock — self-docking validation

All acd dock options

🐍 Python API

🌐 Streamlit Web App

☁️ Streamlit via Google Colab

📓 Colab Notebook (batch docking)

🖥️ Run Streamlit locally

Linux (Ubuntu/Debian)

macOS

Windows

Streamlit Cloud deployment

✨ What it does

🗺️ 2D Interaction Diagrams

🧬 Anyone Can Dock 2D Diagram (default)

🔬 RDKit 2D Diagram

🔬 PoseView (proteins.plus)

🧬 Supported protein types

♻️ Redocking validation

💻 Platform compatibility

🧬 pKaNET microstate selection

⚗️ Water, cofactor & metal options

📄 Citation

📜 License

About

Resources

Stars

Watchers

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Releases

Packages

Contributors

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⌨️ CLI — `acd` command

`acd redock` — self-docking validation

All `acd dock` options