Library 3

[Jean-Claude Bradley]

It turns out that the the last docking run against falcipain

 http://usefulchem.wikispaces.com/D-EXP012

did not generate enough compounds that we generate economically so we'll have to redo the run with UCLib003

http://usefulchem.wikispaces.com/UClib003

, containing only compounds that we already have in the lab in abundance (>5g)

 

So far the list is still empty because the wrong sheet got updated.

http://spreadsheets.google.com/pub?key=plwwufp30hfpUERhse9y5Kw

 

That is supposed to be to record the experiments that have already been done, noting which ones have a precipitate.

 

This is the sheet which is supposed to be updated for library 3 (notice how the title is UClib003sources)?

http://spreadsheets.google.com/pub?key=plwwufp30hfpCwcPqSZzlDw

 

This is by far our most urgent task and should not take that long to complete.  Anyone who is available today to process use ChemSpider to conver the names to SMILES.  Of course the first task is to copy over all the compounds from the first sheet to the second.  I'm assuming that the compounds listed there are all that we have at least 5g or 5 mL - Khalid if that is not the case then please fix that. 

 

Let me know if you are having trouble processing the names to SMILES using ChemSpider.

--
Jean-Claude Bradley, Ph. D.
E-Learning Coordinator for the College of Arts and Sciences
Associate Professor of Chemistry
Drexel University

http://drexel-coas-elearning.blogspot.com
http://drexel-coas-talks-mp3-podcast.blogspot.com/
http://usefulchem.blogspot.com

[jcb]

Rajarshi,
We are getting a Python error when trying to generate this 73K library
using the SMILES and algorithm listed here
http://usefulchem.wikispaces.com/UClib003

Is the chirality info @, @@ causing a problem?

Jean-Claude

On Oct 6, 10:43 am, "Jean-Claude Bradley"

<jeanclaude.brad...@gmail.com> wrote:
> It turns out that the the last docking run against falcipain
> http://usefulchem.wikispaces.com/D-EXP012
> did not generate enough compounds that we generate economically so we'll

> have to redo the run with UCLib003http://usefulchem.wikispaces.com/UClib003

> , containing only compounds that we already have in the lab in abundance
> (>5g)
>

> So far the list is still empty because the wrong sheet got updated.http://spreadsheets.google.com/pub?key=plwwufp30hfpUERhse9y5Kw

>
> That is supposed to be to record the experiments that have already been
> done, noting which ones have a precipitate.
>
> This is the sheet which is supposed to be updated for library 3 (notice how

> the title is UClib003sources)?http://spreadsheets.google.com/pub?key=plwwufp30hfpCwcPqSZzlDw

[Rajarshi]

On Oct 8, 8:41 am, jcb <jeanclaude.brad...@gmail.com> wrote:
> Rajarshi,
> We are getting a Python error when trying to generate this 73K library

> using the SMILES and algorithm listed herehttp://usefulchem.wikispaces.com/UClib003

>
> Is the chirality info @, @@ causing a problem?

No, it's a text encoding issue. Undecylic acid and 4-
chlorophenylacetic acid have strange characters, if you look at them
in Notepad or any plain text editor.

After fixing those, the service works fine and gives ~61K compounds.

I've updated the error messages so that they're more meaningful

[Jean-Claude Bradley]

Rajarshi,

Thanks!  We'll try again with the fixed SMILES.

Your number is lower than my calculation - could that be because your code automatically detects duplicates or does it sometimes skip some molecules?

 

--
Jean-Claude Bradley, Ph. D.
E-Learning Coordinator for the College of Arts and Sciences
Associate Professor of Chemistry
Drexel University

[Rajarshi]

On Oct 8, 12:24 pm, "Jean-Claude Bradley"

<jeanclaude.brad...@gmail.com> wrote:
> Rajarshi,
> Thanks! We'll try again with the fixed SMILES.
> Your number is lower than my calculation - could that be because your code
> automatically detects duplicates or does it sometimes skip some molecules?

Yes, it'll skip some of the input reagents. I didn't check very
closely, but the skipped molecules are reported on the download page

[Jean-Claude Bradley]

Thanks - Khalid when you run it again note which ones it skipped please.

On 10/8/07, Rajarshi <rajars...@gmail.com> wrote:

[Khalid Mirza]

Combinatorial Library Generation - Ugi Reaction - Results

Get virtual library [64638 compounds]

Skipped acids
O=C(OO)C1=CC(Cl)=CC=C1 -----3-chlorobenzoic acid
(cc(C(O)=O)c1O)[N+]([O-])=O----5-nitrosalicylic acid
CCCCCCCCCCCCCCCC(=O)OH----palmitic acid
CCC(C(=O)[O-])OC1=CC=CC=C1-----α-phenoxybutyric acid
C1=CC(=C(C=C1C(=O)O)[N+](=O)[O-])C(=O)O-----nitroterephthalic acid
CCCCCCCC\C=C/CCCCCCC(OH)=O-----oleic acid
OC(=O)C(F)(F)C(F)(F)C(F)(F)C (F)(F)C(F)(F)C(F)(F)C(F)(F)F-----perfluorooctanoic acid

--
Khalid Mirza
Graduate Student
The Bradley Research Group
Department of Chemistry
Drexel University
usefulchem.wikispaces.com

[Rajarshi]

On Oct 8, 5:30 pm, "Khalid Mirza" <khalidsmi...@gmail.com> wrote:

> *Skipped acids*
> O=C(OO)C1=CC(Cl)=CC=C1 -----3-chlorobenzoic acid

This looks like a peroxy acid

> (cc(C(O)=O)c1O)[N+]([O-])=O----5-nitrosalicylic acid

invalid smiles (daylight depict wont display it)

> CCCCCCCCCCCCCCCC(=O)OH----palmitic acid
> CCC(C(=O)[O-])OC1=CC=CC=C1-----α-phenoxybutyric acid
> C1=CC(=C(C=C1C(=O)O)[N+](=O)[O-])C(=O)O-----nitroterephthalic acid
> CCCCCCCC\C=C/CCCCCCC(OH)=O-----oleic acid
> OC(=O)C(F)(F)C(F)(F)C(F)(F)C
> (F)(F)C(F)(F)C(F)(F)C(F)(F)F-----perfluorooctanoic acid
>

For the others, it looks like SMILES are in salt form. You should
rpovide neutral SMILES

[Jean-Claude Bradley]

Rajarshi - your code does nicely catch these errors.

 

To make it easier to not let these slip through in the first place, can you recommend a SMILES viewer that converts a list of SMILES into images and checks for validity?  Something like DEPICT that can process lists instead of single entries would be perfect:

http://www.daylight.com/daycgi/depict

 

Jean-Claude

 

On 10/8/07, Rajarshi <rajars...@gmail.com> wrote:

[Rajarshi]

On Oct 9, 5:52 am, "Jean-Claude Bradley"

<jeanclaude.brad...@gmail.com> wrote:
> Rajarshi - your code does nicely catch these errors.
>
> To make it easier to not let these slip through in the first place, can you
> recommend a SMILES viewer that converts a list of SMILES into images and
> checks for validity? Something like DEPICT that can process lists instead
> of single entries would be perfect:http://www.daylight.com/daycgi/depict

Well a kludgy workaround is to use the Daylight depict match page
which is used for testing SMARTS So you can paste all your SMILES and
supply a valid SMARTS string (like C).

http://www.daylight.com/daycgi_tutorials/depictmatch.cgi

I see a CDK application coming in the future ...

[Jean-Claude Bradley]

Rajarshi,

Ok - it looks like everything ran fine to create Library 3.

Could you please run it against V1 and V2 on falcipain-2 as you did previously?

The details (including the link to the library) are here:

http://usefulchem.wikispaces.com/D-EXP014

 

I copied over what  I think is still applicable - please edit or let me know if it is not.

Thanks!

Jean-Claude

--
Jean-Claude Bradley, Ph. D.
E-Learning Coordinator for the College of Arts and Sciences

[Rajarshi]

On Oct 9, 4:18 pm, "Jean-Claude Bradley"

<jeanclaude.brad...@gmail.com> wrote:
> Rajarshi,
> Ok - it looks like everything ran fine to create Library 3.
> Could you please run it against V1 and V2 on falcipain-2 as you did
> previously?

The results are available at http://rguha.ath.cx/~rguha/cicc/fpdock/003/

[Jean-Claude Bradley]

Thanks Rajarshi!  OK UsefulChem lab group  - you know what to do - make those compounds!