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Contents
 
Introduction
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PrevICM User's Guide
15.11 Impose Tethers or Distance Restraints
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[ Tether | Distance Restraint ]

Available in the following product(s): ICM-Pro | ICM-VLS | ICM-Chemist-Pro

15.11.1 Impose Ligand Atom Tether


To impose tethers to selected atoms of the ligand before redocking.

  • Setup the ligand and receptor.
  • Click on the edit tools panel button.
  • Click on the impose positional restraints button.
  • Select the atoms you wish to tether in the ligand.
  • A table listing the tethers will be displayed and red crosses through the atom indicates a tether.
  • Click on the re-dock button and the atoms selected will remain tethered in place.

About the table: The tethers can be edited and deleted using the table. Double click on a value in the table to edit it.

  • Use Check "use" to use the tether in docking.
  • L Toggle the tether display on or off.
  • Type Type of tether "position" indicates a positiional restraint (tether).
  • Atom1 ICM selction language for the tethered atom. Atom 1 can also be SMARTS expression which define the atom (for both distance and position) The matched atom should be marked with '*'. For example oxygen in the double bonded to the 5-member ring in biotin can be defined as: NC(=[O*])N
  • Atom2 xyz position (3 comma separated numbers)
  • max dist Sets the maximum distance for the tether.
  • min dist Sets the minimum distance for the tether.
  • weight the overall weighting factor for the tether penalty term.
  • rm Delete the tether.
  • err Deviation from the position after docking.

15.11.2 Impose Distance Restraint


There are three types of distance restraint you can make:

  1. lig - static rec : fixed side-chain (weighted tether)
  2. lig - flex rec : flexible side-chain (drestraint)
  3. lig - lig : drestrains

To impose distance restraints before redocking.

  • Setup the ligand and receptor.
  • Click on the edit tools panel button.
  • Click on the distance restraint button.
  • Select two atoms to form the distance restraint. The distance restraint can be between two atoms in a ligand or between the ligand and receptor
  • A table detailing the distance restrints will be displayed and red crosses through the atom indicates a tether.
  • Click on the re-dock button and the atoms selected will remain tethered in place.

About the table: The distance restraints can be edited and deleted using the table. Double click on a value in the table to edit it.

  • Use Check "use" to use the distance restraint in docking.
  • L Toggle the distance restraint display on or off.
  • Type Type of restraint. There are three types of distance restraint
    1. lig - static rec : fixed side-chain (weighted tether)
    2. lig - flex rec : flexible side-chain (drestraint)
    3. lig - lig : (drestraint)
  • Atom1 ICM selction language for the first atom in the distance restraint.
  • Atom2 ICM selction language for the second atom in the distance restraint.
  • max dist Sets the maximum distance for the restraint.
  • min dist Sets the minimum distance for the restraint.
  • weight the overall weighting factor for the distance restraint penalty term.
  • rm Delete the distance restraint.
  • err Deviation from the position after docking.

Note: The area within min-max distance is zero (flat-bottomed). With a weight of 1. you will have fair coverage of conformations with minor violations, going up to 5 or 10 will pretty much force the system to always stay there, below 1. you will only have a sort of weak steering force.


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