How to compute molecular properties like logP & logD - hydrophobicity



  • 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



  • 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).



  • @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?



  • @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.



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


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