Hi Brian. Unfortunately, I haven't gotten any additional responses. This
isn't a topic you've looked into, is it? Thanks!

On Mon, Oct 16, 2017, 3:37 PM Bennion, Brian <benni...@llnl.gov> wrote:

> Hello Jacob,
>
> Have you received any offline replies to this post?
>
> brian
>
>
> ------------------------------
> *From:* Jacob D Durrant <durra...@pitt.edu>
> *Sent:* Thursday, October 12, 2017 10:21:46 PM
> *To:* rdkit-discuss@lists.sourceforge.net
> *Subject:* [Rdkit-discuss] Question about pKa prediction using RDKit
>
> I've been struggling to implement the SMARTS-based pKa prediction
> algorithm outlined by Crippen here:
> http://pubs.acs.org/doi/abs/10.1021/ci8001815
> <https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fpubs.acs.org%2Fdoi%2Fabs%2F10.1021%2Fci8001815&data=01%7C01%7Cdurrantj%40pitt.edu%7C9c4fd212d3c841e53cf108d514cd5eee%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=7bEn4YSQZrTDKAEfvg%2BTKhYEOnGTQYlZiQOvRTcPO4Q%3D&reserved=0>
>
> This same method has been mentioned elsewhere on this forum:
> https://sourceforge.net/p/rdkit/mailman/message/27318424/
> <https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsourceforge.net%2Fp%2Frdkit%2Fmailman%2Fmessage%2F27318424%2F&data=01%7C01%7Cdurrantj%40pitt.edu%7C9c4fd212d3c841e53cf108d514cd5eee%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=p6uuRMfIjUilI%2BA%2BV3nd3TXNbuK3HanhCG2XiHGv%2Bhg%3D&reserved=0>
>  ;
> http://rdkit-discuss.narkive.com/jOHraNs8/crippen-pka-model-in-rdkit
> <https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Frdkit-discuss.narkive.com%2FjOHraNs8%2Fcrippen-pka-model-in-rdkit&data=01%7C01%7Cdurrantj%40pitt.edu%7C9c4fd212d3c841e53cf108d514cd5eee%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=iSNXaRzibhcEUwfQg%2FjY%2BjFC26CQaB0NYlxPxJA3R8M%3D&reserved=0>
>
> Am I right in thinking that this method has never been successfully
> implemented?
>
> Assuming not, I'm wondering if anyone else has had a hard time reproducing
> the values listed in that paper's SI using the provided decision tree. For
> example, consider the compound O(C)c1cc(ccc1OC)C(=O)C(O)=O
>
> Running through the decision tree:
>
> Node 2: Does contain [#G6H]C(=O)
> Node 4: Does contain [OH][i](=O)*(~*)~*
> Node 8: Does contain a[#X]
> Node 16: Does contain *~*~*~*~*~*~*~*~*
> Node 32: Does contain [i][#G6v2]
> Node 64: Does contain [O][i]~[i]~[i]~[i]~[i]~[i]~[i]~[A]
> Node 129: Does not contain [OH][i]~[i]~[i]~[i]-*
> Node 258: Does contain [OH][i](=O)[i]~[i]~[i]~[i]-*
>           Terminal node. 3.1849999 (2.79)
>
> And yet the paper lists the decision-tree output for that molecule as 1.8.
>
> Am I missing something obvious? I'd appreciate any help the community
> could offer. Having a basic pKa predictor in rdkit would be so useful...
>
> Thanks!
>
>
>
> --
>
> Sent from my mobile.
>
-- 

Sent from my mobile.
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