Use DiffDock-L

Official Neurosnap webserver for accessing DiffDock-L online.

Molecular Docking Drug Design

Overview

DiffDock-L is the newer and better version of DiffDock, a state of the art method for molecular docking and drug binding structure prediction. This service uses DiffDock-L and AutoDock VINA to predict protein-ligand interactions with high accuracy.

Neurosnap Overview

The DiffDock-L online webserver allows anybody with a Neurosnap account to run and access DiffDock-L, no downloads required. Information submitted through this webserver is kept confidential and never sold to third parties as detailed by our strong terms of service and privacy policy.

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Features

  • Utilizes the improved DiffDock-L implementation.
  • Predict ligand binding to a protein target of interest.
  • Can be used for drug design as well as domain identification.
  • Includes an interactive 3D protein viewer with the docked ligand.

Configuration & Options

Model Inputs

Allowed Types: pdb
The PDB structure of the protein you want to bind a ligand to. Input structures must be under 2048 amino acids. For best results ensure your structure is under 1022 amino acids as DiffDock-L was not trained on proteins exceeding 1022 amino acids. DiffDock does not currently support small molecules, ligands, and nucleotides within the receptor structure.

Allowed Types: sdf or pdb
The chemical structure of the ligand you want to bind. For PDB files ensure that your protein/peptide is 40 residues or less and only contains a single chain / molecule.

Alternatively, if your ligand file isn't working you can enter a corresponding SMILES string here for your input ligand. You can create a SMILES string for your molecule using https://www.cheminfo.org/flavor/malaria/Utilities/SMILES_generator___checker/index.html

The number of samples/predictions for the model to produce. Larger amounts will result in greater wait times, but more comprehensive results (recommended).

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