ChemAxon 60613ab728
17-01-2008 07:59:49
Thank you in advance,
Miklos
ChemAxon 60613ab728
17-01-2008 07:59:49
User 851ac690a0
18-01-2008 09:59:51
ChemAxon 60613ab728
19-03-2009 12:00:08
User 851ac690a0
23-03-2009 07:21:46
Quote: |
Is this correct? |
Quote: |
Is there any way to customize the donor-acceptor rules in Chemaxon? |
User 331d7f5c0b
25-08-2009 04:30:45
Jozsi wrote: |
Hi, Acceptor atoms have to have a lone-pair electron. A donor atom is connected with at least one H atom. Additional useful details are given by Kubinyi. For example in these two references: http://www.beilstein-institut.de/bozen2004/proceedings/Kubinyi/Kubinyi.htm http://www.kubinyi.de/dd-18.pdf Basically we accepted Kubinyi's results in our implementation. Donor and Acceptor counts depend on the pH ( pKa ). This type of calculation was also implemented in our java package. Cheers, Jozsi |
Hi Jozsi,
Is this still the algorithm that ChemAxon uses? Also, it might be good to note somewhere that this method is not the one Lipinski uses in the Rule of 5:
"There are more than 5 H-bond donors (expressed as the sum of OHs and NHs);
The MWT is over 500;
The Log P is over 5 (or MLogP is over 4.15);
There are more than 10 H-bond acceptors (expressed as the sum of Ns and Os);"
Best regards,
Moses
User 851ac690a0
25-08-2009 11:12:13
Hi,
1.
I described in the above part how donors and acceptors are defined in Marvin. I think they are defined correctly in Marvin. Don't you think so?
2.
Lipinski rule of 5 requires only a subset of potential donor and acceptor centers. Only "Oxygen" and "Nitrogen" included in this subset.
Did you find any bug or problem with the Lipinski rule of 5 implemented by us?
Jozsi
ChemAxon e08c317633
25-08-2009 11:48:33
moses wrote: |
Is this still the algorithm that ChemAxon uses? Also, it might be good to note somewhere that this method is not the one Lipinski uses in the Rule of 5: "There are more than 5 H-bond donors (expressed as the sum of OHs and NHs); Best regards, Moses |
Hi Moses,
I think the quoted definition of Lipinski's Rule of 5 is not correct.
Lipinski's rule says that, in general, an orally active drug has no more than one violation of the following criteria:
The corresponding Chemical Terms expression is:
(mass() <= 500) && (logP() <= 5) && ((disjointMatchCount('N[H]') + disjointMatchCount('O[H]')) <= 5) && ((atomCount('7') + atomCount('8')) <= 10)
I hope this helps.
Zsolt
User 331d7f5c0b
25-08-2009 18:37:41
Jozsi wrote: |
Hi, Hi Jozsi: I'm actually not a computational chemist, so I'm not qualified to say whether it's right, but I'm sure you guys are on top of it. My question was simply whether you still use that algorithm, so that we can forward it to customers when they ask us what algorithm is used. As far as whether the rule of 5 is implemented correctly, you don't have an explicit chemical terms expression for it (i.e. ruleOfFive() or something like that), so there's nothing wrong there. My comment was only that you might want to note somewhere that donorCount() and acceptorCount() are not for use with the Lipinski Rule of 5, because he used a simplified donor/acceptor count algorithm, and if you don't use that algorithm the statistics on which the Rule of 5 is based don't come out the same. Also, I've noticed that in Instant JChem the rule of 5 provided as a "favorite chemical terms expresion" when adding a new chemical terms column does use donorCount() and acceptorCount(). So, just to follow up with a clearer question: Do you still use that algorithm, so we can tell our customers that's the algorithm used for donorCount() and acceptorCount()? Moses |
User 331d7f5c0b
25-08-2009 18:39:45
Zsolt wrote: | ||
Hi Moses, I think the quoted definition of Lipinski's Rule of 5 is not correct. Lipinski's rule says that, in general, an orally active drug has no more than one violation of the following criteria:
The corresponding Chemical Terms expression is: (mass() <= 500) && (logP() <= 5) && ((disjointMatchCount('N[H]') + disjointMatchCount('O[H]')) <= 5) && ((atomCount('7') + atomCount('8')) <= 10) I hope this helps. Zsolt |
Hi Zsolt,
Actually that quote of Lipinski's rule was straight out of his original paper, so I think it's correct. However, your restating of the rule seems to be exactly the same? So I think we're on the same page, I think... : )
Your chemical terms expression is correct, thanks for the pointer on disjointMatchCount().
Moses
ChemAxon e08c317633
25-08-2009 19:07:22
moses wrote: | ||||
Hi Zsolt, Actually that quote of Lipinski's rule was straight out of his original paper, so I think it's correct. However, your restating of the rule seems to be exactly the same? So I think we're on the same page, I think... : ) Your chemical terms expression is correct, thanks for the pointer on disjointMatchCount(). Moses |
Yes, we are on the same page.
Your quotation: "There are more than 5 H-bond donors (expressed as the sum of OHs and NHs)"
Usually used as: "Not more than 5 hydrogen bond donors (nitrogen or oxygen atoms with one or more hydrogen atoms)"
Same for the other criteria (molecular weight under/over 500, etc.). It's just some clarification for others forum users, who might get confused.
Regards,
Zsolt
User 851ac690a0
25-08-2009 23:00:46
Hi Moses,
donorCount() and acceptorCount() are not for use
with the Lipinski Rule of 5, because he used a simplified
donor/acceptor count algorithm
Yes , you are right. We need to emphasize this fact anywhere in the documentation.
... Instant JChem the rule of 5 ...when adding a new chemical terms column does use donorCount() and acceptorCount().
...Do you still use that
algorithm, so we can tell our customers that's the algorithm used for
donorCount() and acceptorCount()?
I can check this tomorrow. I get back asap.
Thanks!
Jozsi
User 851ac690a0
26-08-2009 11:25:46
Hi,
Do you still use that algorithm...
Yes.
Jozsi
User 68ba94adee
21-05-2015 18:48:50
mjszabo wrote: |
Could you please describe what is the exact rule for counting Hydrogen Bond Donors and Acceptors in Chemaxon applications? Which atoms/groups are involved in the rules? Thank you in advance, Miklos |
Plz tell the difference between hydrogen bond acceptor counts and sites. Are they same?? plz explain the in detail
ChemAxon d51151248d
22-05-2015 11:54:20
Hi,
I link here an older forum topic where you can find the description between donor/acceptor sites and count:
https://www.chemaxon.com/forum/ftopic5983.html
I hope this helps.
Daniel
User 771e0d9901
14-11-2015 10:59:01
danielszisz wrote: |
Hi, I link here an older forum topic where you can find the description between donor/acceptor sites and count: https://www.chemaxon.com/forum/ftopic5983.html I hope this helps. Daniel |
thanks for your help. It's useful
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User a6e5e950b8
20-04-2016 09:16:47
And since oxygen is not acceptor in furan ring this is why sulphur can not act as an acceptor in thiophene ring.????
ChemAxon d51151248d
20-04-2016 12:40:07
Hi,
Recognizing S as an acceptor atom can be set as an option in the HBDA Plugin. In aromatic rings neither S nor O atoms are allowed to be an acceptor atom. It is not usual for the S to behave as an acceptor in an aromatic ring.
However, if you have any scientific references to support that idea, we would be happy to have it.
Daniel