CovalentDock Cloud

Create a new docking job.

Sample Input:

Currently the CovalentDock package support covalent docking adopting the following two mechanisms. Use the buttons to automatically setup parameters for the sample covalent docking experiment.

Michael additions

Receptor: ERK-2 (PDB: 3C9W)
Binding site: CYS-164
Ligand: Hypothemycin (ZINC: 34034438)

Additions to β-lactam

Receptor: β-lactamase (PDB: 1GHP)
Binding site: SER-70
Ligand: Penicillin (ZINC: 3871701)

Receptor:

Please use one of the following methods to setup the receptor.


The receptor structure will be retrieved from PDB and cleaned automatically. The automatically retrieved receptor may not be ready for docking, in such cases, please prepare the structure manually and upload it.

or

The uploaded receptor will be used as-is. Please prepare the structure coordiningly before submission, check the Help page for instructions.

Binding site:

Please use one of the following methods to specify the covalent binding site. If you need a visualization tool to help choosing the binding site, feel free to try this basic receptor explorer.

Please specify the covalent binding site by selecting the residue type, entering its sequence number and the chain identifier. The chain identifier is optional and defaulted to the first chain appears in the PDB.

or


Please enter the coordinates of the CENTER of the binding site. '0, 0, 0' or other random/inaccurate coordinates may not get the satisfactory results, or the docking protocol may fail before successful termination.

Ligand:

Please use one of the following methods to setup the ligand.

The ligand structure will be retrieved from ZINC and preprocessed automatically. The automatically retrieved ligand may not be ready for docking, in such cases, please prepare the structure manually and upload it.

or

Please upload an INTACT ligand structure (i.e. the structure prior any change brought by covalent linkage formation). The uploaded ligand will be used as-is. Please prepare the structure coordingly before submission, check the Help page for instructions.

  • Currently the backend CovalentDock program supports two types of covalent binding: Michael additions (Type-I) and β-lactam reactions (Type-II). Supports to additional reaction types are now under development and will be integrated into this web server in near future.
  • Please make sure that there is at least one covalent linking residue within the binding site. For Type-I binding, it's a Cysteine; for Type-II binding, it's a Serine. Otherwise the docking program will refuse to start.
  • Please also make sure that there is at least one covalent linking pattern in the ligand structure. For Type-I binding, it's a Michael acceptor; for Type-II binding, it's a β-lactam group. Otherwise the docking program will also refuse to start.
  • For more information, please go to the Help page.