1.3.0.0

New Job Submission


1. Job Settings (Optional)
2. Select Script
Description:
Unconstrainded ligand exploration an binding site search

This script explores the entire space and locates different binding sites for the ligand.

Ligand must be present in the uploaded PDB file as HETATM records. The ligand chain and residue IDs and Number of steps must be set below.

After completion, program returns the PDB files (accepted steps). The log file will have the total energy and the binding energies. If a native reference structure is provided, the log file returns the ligand heavy atom RMSD to the native, otherwise to the initial structure.

Sample PDB

Aspirin binding to the Phospholipase A2 (PDB ID: 1OXR) is used as the Sample PDB. The animation to the left of this box shows 67 accepted steps of a typical trajectory generated by the default parameters with waters (red dots) and calcium ion (cyan) present. You can find longer video of another simulation run of this sample in the Examples section along with the control script and the trajectory files.

In order to include waters and calcium ion (also included in the sample PDB), you must set 'Read ions' and 'Read waters' items below to 'yes'.

Using 16 CPUs, the near native pose (RMSD less than 2.0 Å) can be found in an hour.

References
  1. PELE: Protein energy landscape exploration. A novel Monte Carlo based technique [J. Chem. Theo. Comput., 1(6):1304-1311 (2005)]
  2. Exploring hierarchical refinement techniques for induced fit docking with protein and ligand flexibility [J. Comput. Chem., 1(31):1224-1235 (2010)]
3. Select File
PDB File:
Native:(Optional)
Control File:
4. Preparing the Input File (Optional)
5. Set Required Metrics for the Output (Optional)
6. Ligand Free Exploration Settings (Optional)