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I'm generating random molecules I would like to know if they are able to pass through the cell membrane. Are there any ways (preferably computational) to predict cellular uptake of an organic molecule which is about 55 atoms?

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If it's polar, it's not going through. If it's non-polar, there's a good chance it will diffuse through... –  Chinmay Kanchi May 26 '13 at 17:42
    
cLogP? I would imagine that's a fast dirty way to get an estimate. en.wikipedia.org/wiki/Partition_coefficient –  bobthejoe May 28 '13 at 20:59
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Absorption, distribution, metabolism, excretion, and toxicity ADMET can be somewhat computationally defined but is largely secretive due to the money involved in drug discovery. FAF-Drugs2 will do basic ADMET. The Schordinger Suit provides a more indepth ADMET for a fee.

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