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Probe Molecules

Probe molecules and their fractional composition, shown below, were selected based on analysis of FDA approved drugs [AB12]_. The best composition for a specific system may, however, depend on the surface properties of the target. For a protein with a highly charged surface, increasing the proportion of acetate and isopropylamine might perform better in identifying ligandable sites.

.. only:: html

   +----------------------------+----------------------------+----------------------------+
   |.. figure:: _static/ipro.png|.. figure:: _static/acam.png|.. figure:: _static/acet.png|
   |   :scale: 25%              |   :scale: 25%              |   :scale: 25%              |
   |                            |                            |                            |
   |   Isopropanol (70%)        |   Acetamide (10%)          |   Acetate (10%)            |
   +----------------------------+----------------------------+----------------------------+
   |.. figure:: _static/ipam.png|.. figure:: _static/ibut.png|                            |
   |   :scale: 25%              |   :scale: 25%              |                            |
   |                            |                            |                            |
   |   Isopropylamine (10%)     |   Isobutane (0%)           |                            |
   +----------------------------+----------------------------+----------------------------+


.. only:: latex

   .. figure:: _static/ipro.png
      :scale: 25%

      Isopropanol (70%)

   .. figure:: _static/acam.png
      :scale: 25%

      Acetamide (10%)

   .. figure:: _static/acet.png
      :scale: 25%

      Acetate (10%)

   .. figure:: _static/ipam.png
      :scale: 25%

      Isopropylamine (10%)

   .. figure:: _static/ibut.png
      :scale: 25%

      Isobutane (0%)

Among these, isobutane is not included in the default configuration due to its high propensity to aggregate. If it is included, it should have a small fraction.

Topology & Parameter

Probe atom types and parameters are based on protein side-chains described in CHARMM force field. Below topology and parameter files distributed with the plugin are shown:

.. literalinclude:: drugui/probe.top


.. literalinclude:: drugui/probe.prm