What is the difference between Core and Positional constraints? Which do I use if I want to positionally constrain the core of my molecule?

A positional constraint requires that a ligand atom (of a type defined by the SMARTS patterns in the ligand feature definition) be located within a user-specified distance of the positional constraint sphere center. A core constraint requires that a ligand with the same core as a reference molecule (defined by SMARTS) dock such that its core lies within a user-specified RMSD tolerance of the reference core.

If you want to constrain the core of a molecule to be similar to a reference molecule or pose, you should use the RMSD-based core constraint, rather than positional constraints. A positional constraint is a distance constraint applied to an individual atom, so multiple such constraints would have to be applied in order to enforce a particular desired spatial orientation of a set of core atoms. In addition to being more difficult to set up than a core constraint, multiple positional constraints might allow undesired solutions if the constraint spheres overlap both spatially and in their allowed ligand features.

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