Galaxy |

Run OpenDUck (version 0.1.1)

PDB file for apoprotein:

Chunk (in PDB format):

PDB file produced by chunk tool.

SDF/MOL file containing a single ligand:

Parameters for the protein-ligand interactions

Parameters for the protein-ligand interaction 0

MD run length (ns):

Length of initial MD run (prior to steered molecular dynamics runs).

Starting distance:

Initial length of the selected interaction between protein and ligand.

Number of SMD runs:

Number of steered molecular dynamics runs to perform.

Velocity:

Distance (in angstroms) to perturb the system per simulation step in the SMD runs. Decreasing this value will increase simulation time.

Return a tar file?:

Return a tar file containing all files produced during the simulations.

What it does

Perform steered molecular dynamics runs for dynamic undocking (DUck), performing system preparation (topology calculation and minimization), an initial MD run, and SMD runs.

This Galaxy tool uses OpenDUck, an open-source implementation of the original DUck method, using OpenMM and AmberTools.

Input

PDB file for apoprotein

PDB file for chunk

SDF/MOL file for ligand

Parameters defining the protein-ligand interaction

Parameters for MD and SMD runs

Output

Ligand in SDF/MOL format, with added <SCORE.DUCK_WQB> parameter.

A tar file is also produced as a optional output, containing all files produced by the tool.