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    How to compute molecular properties like logP & logD - hydrophobicity

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    • T
      Thanos last edited by

      Hi all,

      I have created a drug design and I would like to calculate its logP and logD properties and get in general a better understanding on which drug delivery carriers are appropriate for this design. Do I have to run a simulation or sth to calculate properties like these? Is there an app in general that can give me more info on drug delivery?

      Kind regards,
      Thanos Pasias

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      • DmitriyMarin
        DmitriyMarin last edited by

        Hello @Thanos ,

        As far as I know, there is no app that computes logP and logD properties. But if you want to visualize the hydrophobicity of a protein you can do this by applying a hydrophobicity color scheme (you can also change the hydrophobicity scales).

        Dmitriy,
        The SAMSON Team, https://s-c.io

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          Thanos @DmitriyMarin last edited by

          @dmitriymarin Hi! Thank you for your reply. I didn't know that, this is the first time I do this :) thanks. I have found the hydrophobicity button, is the red color more or less hydrophobic? Also how does the polarity color palette work? The darker the color the greater the polarity is?

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          • DmitriyMarin
            DmitriyMarin @Thanos last edited by DmitriyMarin

            @thanos For hydrophobicity: blue is the minimum value of hydrophobicity (more hydrophilic - hence blue) and red is the maximum value of hydrophobicity.
            0_1585511485795_36b77e1e-7fd7-4c74-ba32-488bb10d51af-image.png

            As for the polarity, the colors are just descriptive - to differentiate between the types of the side chain polarity: non polar, polar, acidic polar, basic polar.
            In the default color scheme: nonpolar - violet, polar - light blue, acidic polar - light green, basic polar - yellow.
            0_1585511522064_91322d2d-d2a6-49f5-a35a-ef17a47425a6-image.png
            You can see it through the Inspector when selecting a residue:
            0_1585511401874_10163600-3376-4db7-b47f-fd13cc191922-image.png
            In the next update of SAMSON, it would be possible to select the color palettes.

            Dmitriy,
            The SAMSON Team, https://s-c.io

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              Thanos @DmitriyMarin last edited by

              @dmitriymarin Wow this is really great, thank you!!!

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