Tools for docking prep

• Protein → PDB ID

  Search PDB by Protein Name

  Find high-resolution PDB IDs from a protein name (EGFR, ACE2, HER2) and dock in one click.

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  • Name to SMILES — Name → SMILES
  • PDB Cleaner — PDB → Clean receptor
  • PDBQT Converter — PDB → PDBQT

• Name → SMILES

  Chemical Name to SMILES

  Convert drug or IUPAC names into Canonical SMILES via PubChem — ready for AutoDock Vina.

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  • SMILES Converter — SMILES ↔ SDF
  • Rule of 5 — SMILES → Drug-likeness
  • PDBQT Converter — PDB → PDBQT

• SMILES ↔ SDF

  SMILES Converter

  Convert SMILES to SDF or MOL, or turn SDF, MOL, and PDB back into SMILES — in the browser. Look up a chemical name on the same page.

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  Also useful next

  • Name to SMILES — Name → SMILES
  • PDBQT Converter — PDB → PDBQT
  • Rule of 5 — SMILES → Drug-likeness

• PDB → Clean receptor

  PDB Cleaner — Remove Water & Heteroatoms

  Strip HOH waters and optional HETATM records from a PDB in your browser — docking-ready receptor prep.

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  • PDB Search — Protein → PDB ID
  • PDBQT Converter — PDB → PDBQT
  • Grid Box — Ligand → Box center

• Ligand → Box center

  AutoDock Vina Grid Box Calculator

  Upload a reference ligand PDB/SDF to compute Center X/Y/Z and Size for your Vina search box — copy config.txt in one click.

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  Also useful next

  • PDBQT Converter — PDB → PDBQT
  • PDB Cleaner — PDB → Clean receptor
  • Name to SMILES — Name → SMILES

• SMILES → Drug-likeness

  Lipinski Rule of 5 & Drug-likeness Checker

  Paste SMILES to compute MW, LogP, HBD, and HBA with RDKit.js in-browser — pass/fail Lipinski filter before docking.

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  Also useful next

  • Name to SMILES — Name → SMILES
  • PDBQT Converter — PDB → PDBQT
  • PDB Search — Protein → PDB ID

• PDB → PDBQT

  SMILES / SDF / PDB → PDBQT Converter

  Free PDB to PDBQT online (also SDF/SMILES) with Open Babel — no MGLTools. Download Vina-ready files or dock in the cloud.

  Open

  Also useful next

  • Name to SMILES — Name → SMILES
  • PDB Cleaner — PDB → Clean receptor
  • Grid Box — Ligand → Box center

Worked example: dock SARS-CoV-2 Mpro (PDB 6LU7)

Ready to dock? Open the AutoDock Vina form.