Re: [BlueObelisk-discuss] Software for ligands

[Geoffrey Hutchison]

> I have suggested that there are Open tools that they may not yet have 
> discovered. They have needs for (at least):
>  * 2-D chemical editor and display

I do not think such a thing currently exists. The ChemDoodle tool, while not 
open, is at least low cost, and they do support open source web components 
(http://web.chemdoodle.com/)

This is a sorely lacking area.

>  * 3-D editor 

I humbly suggest Avogadro. :-)

> I am not up-to-date with all the Open software. Do we have a list of tools in 
> this area? If not, perhaps people can respond to the list? It would be a 
> useful update.

Multiple people have suggested the recent review, which also lives online (and 
open):
https://opensourcemolecularmodeling.github.io

Cheers,
-Geoff
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Re: [BlueObelisk-discuss] Fwd: Software for ligands

[Paul Emsley]

Hi Peter, Rajarshi and Wibe,

Thanks for your input.

There doesn't seem to be an obvious candidate for the 2D editor. We will 
explore what's available.


Paul (and Garib).


On 18/08/16 17:18, Garib Murshudov wrote:



Begin forwarded message:


*From: *Wibe de Jong mailto:wadej...@lbl.gov>>
*Subject: **Re: [BlueObelisk-discuss] Software for ligands*
*Date: *18 August 2016 17:16:03 BST
*To: *rajarshi.g...@gmail.com 
*Cc: *Peter Murray-Rust mailto:pm...@cam.ac.uk>>, 
BlueObelisk-Discuss >, 
ga...@mrc-lmb.cam.ac.uk 


That's a nice overview paper. Started to look more into descriptors, 
so happy to see the listing of tools one can start from.


Some of the web components have been integrated into MongoChem 
(https://openchemistry.kitware.com/). Here we use a greatly extended 
version of Marcus' Chemical Json (reusing some of the CML naming 
conventions) to generate data and populate a MongoDB. The 
computational chemistry app used here is NWChem, for which we now 
have a CJson writer directly in the code (using an open source son 
fortran writer) and an extensive Python script (which I need to 
integrate into cclib at some point in the near future).


Bert

On Thu, Aug 18, 2016 at 5:06 AM, Rajarshi Guha 
mailto:rajarshi.g...@gmail.com>> wrote:


There is a nice listing of open tools by Pirhadi et al and covers
the spectrum from cheminformatics to computational chemistry

http://www.sciencedirect.com/science/article/pii/S1093326316301188 


On Thu, Aug 18, 2016 at 5:13 AM, Peter Murray-Rust
mailto:pm...@cam.ac.uk>> wrote:

I have been talking with the Computational Crystallography
group in Cambridge/LMB who develop ligand dictionaries for
protein crystallography and are building their system with
Open software (and Open data from Crystallography Open Database).

I have suggested that there are Open tools that they may not
yet have discovered. They have needs for (at least):
 * 2-D chemical editor and display
 * 3-D editor
 * atom typing
 * computational chemistry (e.g. DFT)
 * chemical database software

They have filled some of this themselves, and use RDKIT, but
would benefit from other components. I pointed them at
JChempaint - which has matured a lot since I last used it. I
have also suggested NWChem.

I am not up-to-date with all the Open software. Do we have a
list of tools in this area? If not, perhaps people can
respond to the list? It would be a useful update.


-- 
Peter Murray-Rust

Reader in Molecular Informatics
Unilever Centre, Dep. Of Chemistry
University of Cambridge
CB2 1EW, UK
+44-1223-763069 


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-- 
Rajarshi Guha | http://blog.rguha.net 

NIH Center for Advancing Translational Science


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Dr Garib N Murshudov
MRC-LMB
Francis Crick Avenue
Cambridge
CB2 0QH UK
Web http://www.mrc-lmb.cam.ac.uk,
http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/





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Re: [BlueObelisk-discuss] Software for ligands

[Wibe de Jong]

That's a nice overview paper. Started to look more into descriptors, so
happy to see the listing of tools one can start from.

Some of the web components have been integrated into MongoChem (
https://openchemistry.kitware.com/). Here we use a greatly extended version
of Marcus' Chemical Json (reusing some of the CML naming conventions) to
generate data and populate a MongoDB. The computational chemistry app used
here is NWChem, for which we now have a CJson writer directly in the code
(using an open source son fortran writer) and an extensive Python script
(which I need to integrate into cclib at some point in the near future).

Bert

On Thu, Aug 18, 2016 at 5:06 AM, Rajarshi Guha 
wrote:

> There is a nice listing of open tools by Pirhadi et al and covers the
> spectrum from cheminformatics to computational chemistry
>
> http://www.sciencedirect.com/science/article/pii/S1093326316301188
>
> On Thu, Aug 18, 2016 at 5:13 AM, Peter Murray-Rust 
> wrote:
>
>> I have been talking with the Computational Crystallography group in
>> Cambridge/LMB who develop ligand dictionaries for protein crystallography
>> and are building their system with Open software (and Open data from
>> Crystallography Open Database).
>>
>> I have suggested that there are Open tools that they may not yet have
>> discovered. They have needs for (at least):
>>  * 2-D chemical editor and display
>>  * 3-D editor
>>  * atom typing
>>  * computational chemistry (e.g. DFT)
>>  * chemical database software
>>
>> They have filled some of this themselves, and use RDKIT, but would
>> benefit from other components. I pointed them at JChempaint - which has
>> matured a lot since I last used it. I have also suggested NWChem.
>>
>> I am not up-to-date with all the Open software. Do we have a list of
>> tools in this area? If not, perhaps people can respond to the list? It
>> would be a useful update.
>>
>>
>> --
>> Peter Murray-Rust
>> Reader in Molecular Informatics
>> Unilever Centre, Dep. Of Chemistry
>> University of Cambridge
>> CB2 1EW, UK
>> +44-1223-763069
>>
>> 
>> --
>>
>> ___
>> Blueobelisk-discuss mailing list
>> Blueobelisk-discuss@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss
>>
>>
>
>
> --
> Rajarshi Guha | http://blog.rguha.net
> NIH Center for Advancing Translational Science
>
> 
> --
>
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[BlueObelisk-discuss] Fall ACS Meeting BO dinner?

[Robert Belford]

Hi All,

Is anyone going to the ACS meeting and interested in having a BO dinner? I
am running a symposium Sunday morning on "Bringing Cheminformatics into the
Chemistry Classroom", and had an ACS IPG grant in the Spring to bring
students to San Diego where they presented their projects from the Fall
2015 Cheminformatics OLCC, and had $700 left over, which I was going to use
to support a student to the Fall meeting, but his father just had surgery,
and he can't go.  So I got permission to use it for a lunch or dinner.  So
if there is an interest, I can help out with the first $700.

We are also putting together a second offering of the course for the Spring
of 2017, and I think it is turning into a pretty interesting endeavor.  We
are just getting started, and here is the site where this is coming
together,
http://olcc.ccce.divched.org/content/2017-development-site

I should comment that this course is for undergraduate chemistry students,
not computer science students.  We just held a retreat to decide what to
focus on, and I think it is fair to say that our objective is to get
chemistry majors without any programming skills to be able to access public
compound data programmatically.

I am also not sure if you are aware, but the ChemWiki has morphed into
Libretexts, http://chem.libretexts.org/ and we moved the Fall 2015
Cheminformatics
OLCC material to the ChemWiki, and so now all this material is accessible
from organic, biochem and all the other core text of the LibreText
HyperLibrary.

Anyways, is anyone interested in a dinner? We are thinking of a place in
Chinatown, and it probably needs to be on Sunday.  If so, I can help out
with the first $700, and the whole idea of this class came out of a BO
dinner in Boston when Dave Wild and I sat together, and decided to go in on
an education grant.

Cheers,
Bob



-- 
Dr. Robert E. Belford
Associate Professor
UALR Department of Chemistry
501 569-8824
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Re: [BlueObelisk-discuss] Software for ligands

[Greg Landrum]

Orca does indeed look interesting.

For those who care about such things, however, orca is unfortunately not
open-source. It falls into the category that Pirhadi et al. refer to as
"source-available" licenses:
https://orcaforum.cec.mpg.de/license.html


-greg


On Thu, Aug 18, 2016 at 2:38 PM, jay patel  wrote:

> Thanks for referencing Pirhadi et al's recent paper, it looks like one of
> the the most comprehensive list I have come across.
>
> I can highly recommend ORCA (https://orcaforum.cec.mpg.de/) for
> performing all kinds of DFT and ab initio calculations. I have used it on a
> standalone basis as well as with a GUI called gabedit (
> http://gabedit.sourceforge.net/). I saw Pirhadi's paper mention couple of
> other GUI for ORCA too but I haven't had a chance to use it yet.
>
> On Thu, Aug 18, 2016 at 8:06 AM, Rajarshi Guha 
> wrote:
>
>> There is a nice listing of open tools by Pirhadi et al and covers the
>> spectrum from cheminformatics to computational chemistry
>>
>> http://www.sciencedirect.com/science/article/pii/S1093326316301188
>>
>> On Thu, Aug 18, 2016 at 5:13 AM, Peter Murray-Rust 
>> wrote:
>>
>>> I have been talking with the Computational Crystallography group in
>>> Cambridge/LMB who develop ligand dictionaries for protein crystallography
>>> and are building their system with Open software (and Open data from
>>> Crystallography Open Database).
>>>
>>> I have suggested that there are Open tools that they may not yet have
>>> discovered. They have needs for (at least):
>>>  * 2-D chemical editor and display
>>>  * 3-D editor
>>>  * atom typing
>>>  * computational chemistry (e.g. DFT)
>>>  * chemical database software
>>>
>>> They have filled some of this themselves, and use RDKIT, but would
>>> benefit from other components. I pointed them at JChempaint - which has
>>> matured a lot since I last used it. I have also suggested NWChem.
>>>
>>> I am not up-to-date with all the Open software. Do we have a list of
>>> tools in this area? If not, perhaps people can respond to the list? It
>>> would be a useful update.
>>>
>>>
>>> --
>>> Peter Murray-Rust
>>> Reader in Molecular Informatics
>>> Unilever Centre, Dep. Of Chemistry
>>> University of Cambridge
>>> CB2 1EW, UK
>>> +44-1223-763069
>>>
>>> 
>>> --
>>>
>>> ___
>>> Blueobelisk-discuss mailing list
>>> Blueobelisk-discuss@lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss
>>>
>>>
>>
>>
>> --
>> Rajarshi Guha | http://blog.rguha.net
>> NIH Center for Advancing Translational Science
>>
>> 
>> --
>>
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>>
>
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Re: [BlueObelisk-discuss] Software for ligands

[jay patel]

Thanks for referencing Pirhadi et al's recent paper, it looks like one of
the the most comprehensive list I have come across.

I can highly recommend ORCA (https://orcaforum.cec.mpg.de/) for performing
all kinds of DFT and ab initio calculations. I have used it on a standalone
basis as well as with a GUI called gabedit (http://gabedit.sourceforge.net/).
I saw Pirhadi's paper mention couple of other GUI for ORCA too but
I haven't had a chance to use it yet.

On Thu, Aug 18, 2016 at 8:06 AM, Rajarshi Guha 
wrote:

> There is a nice listing of open tools by Pirhadi et al and covers the
> spectrum from cheminformatics to computational chemistry
>
> http://www.sciencedirect.com/science/article/pii/S1093326316301188
>
> On Thu, Aug 18, 2016 at 5:13 AM, Peter Murray-Rust 
> wrote:
>
>> I have been talking with the Computational Crystallography group in
>> Cambridge/LMB who develop ligand dictionaries for protein crystallography
>> and are building their system with Open software (and Open data from
>> Crystallography Open Database).
>>
>> I have suggested that there are Open tools that they may not yet have
>> discovered. They have needs for (at least):
>>  * 2-D chemical editor and display
>>  * 3-D editor
>>  * atom typing
>>  * computational chemistry (e.g. DFT)
>>  * chemical database software
>>
>> They have filled some of this themselves, and use RDKIT, but would
>> benefit from other components. I pointed them at JChempaint - which has
>> matured a lot since I last used it. I have also suggested NWChem.
>>
>> I am not up-to-date with all the Open software. Do we have a list of
>> tools in this area? If not, perhaps people can respond to the list? It
>> would be a useful update.
>>
>>
>> --
>> Peter Murray-Rust
>> Reader in Molecular Informatics
>> Unilever Centre, Dep. Of Chemistry
>> University of Cambridge
>> CB2 1EW, UK
>> +44-1223-763069
>>
>> 
>> --
>>
>> ___
>> Blueobelisk-discuss mailing list
>> Blueobelisk-discuss@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss
>>
>>
>
>
> --
> Rajarshi Guha | http://blog.rguha.net
> NIH Center for Advancing Translational Science
>
> 
> --
>
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Re: [BlueObelisk-discuss] Software for ligands

[Peter Murray-Rust]

Many thanks,

This is impressive! and very welcome to see how much Open Source there is
now.


On Thu, Aug 18, 2016 at 1:06 PM, Rajarshi Guha 
wrote:

> There is a nice listing of open tools by Pirhadi et al and covers the
> spectrum from cheminformatics to computational chemistry
>
> http://www.sciencedirect.com/science/article/pii/S1093326316301188
>
> On Thu, Aug 18, 2016 at 5:13 AM, Peter Murray-Rust 
> wrote:
>
>> I have been talking with the Computational Crystallography group in
>> Cambridge/LMB who develop ligand dictionaries for protein crystallography
>> and are building their system with Open software (and Open data from
>> Crystallography Open Database).
>>
>> I have suggested that there are Open tools that they may not yet have
>> discovered. They have needs for (at least):
>>  * 2-D chemical editor and display
>>  * 3-D editor
>>  * atom typing
>>  * computational chemistry (e.g. DFT)
>>  * chemical database software
>>
>> They have filled some of this themselves, and use RDKIT, but would
>> benefit from other components. I pointed them at JChempaint - which has
>> matured a lot since I last used it. I have also suggested NWChem.
>>
>> I am not up-to-date with all the Open software. Do we have a list of
>> tools in this area? If not, perhaps people can respond to the list? It
>> would be a useful update.
>>
>>
>> --
>> Peter Murray-Rust
>> Reader in Molecular Informatics
>> Unilever Centre, Dep. Of Chemistry
>> University of Cambridge
>> CB2 1EW, UK
>> +44-1223-763069
>>
>> 
>> --
>>
>> ___
>> Blueobelisk-discuss mailing list
>> Blueobelisk-discuss@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss
>>
>>
>
>
> --
> Rajarshi Guha | http://blog.rguha.net
> NIH Center for Advancing Translational Science
>



-- 
Peter Murray-Rust
Reader in Molecular Informatics
Unilever Centre, Dep. Of Chemistry
University of Cambridge
CB2 1EW, UK
+44-1223-763069
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Re: [BlueObelisk-discuss] Software for ligands

[Rajarshi Guha]

There is a nice listing of open tools by Pirhadi et al and covers the
spectrum from cheminformatics to computational chemistry

http://www.sciencedirect.com/science/article/pii/S1093326316301188

On Thu, Aug 18, 2016 at 5:13 AM, Peter Murray-Rust  wrote:

> I have been talking with the Computational Crystallography group in
> Cambridge/LMB who develop ligand dictionaries for protein crystallography
> and are building their system with Open software (and Open data from
> Crystallography Open Database).
>
> I have suggested that there are Open tools that they may not yet have
> discovered. They have needs for (at least):
>  * 2-D chemical editor and display
>  * 3-D editor
>  * atom typing
>  * computational chemistry (e.g. DFT)
>  * chemical database software
>
> They have filled some of this themselves, and use RDKIT, but would benefit
> from other components. I pointed them at JChempaint - which has matured a
> lot since I last used it. I have also suggested NWChem.
>
> I am not up-to-date with all the Open software. Do we have a list of tools
> in this area? If not, perhaps people can respond to the list? It would be a
> useful update.
>
>
> --
> Peter Murray-Rust
> Reader in Molecular Informatics
> Unilever Centre, Dep. Of Chemistry
> University of Cambridge
> CB2 1EW, UK
> +44-1223-763069
>
> 
> --
>
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> https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss
>
>


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NIH Center for Advancing Translational Science
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[BlueObelisk-discuss] Software for ligands

[Peter Murray-Rust]

I have been talking with the Computational Crystallography group in
Cambridge/LMB who develop ligand dictionaries for protein crystallography
and are building their system with Open software (and Open data from
Crystallography Open Database).

I have suggested that there are Open tools that they may not yet have
discovered. They have needs for (at least):
 * 2-D chemical editor and display
 * 3-D editor
 * atom typing
 * computational chemistry (e.g. DFT)
 * chemical database software

They have filled some of this themselves, and use RDKIT, but would benefit
from other components. I pointed them at JChempaint - which has matured a
lot since I last used it. I have also suggested NWChem.

I am not up-to-date with all the Open software. Do we have a list of tools
in this area? If not, perhaps people can respond to the list? It would be a
useful update.


-- 
Peter Murray-Rust
Reader in Molecular Informatics
Unilever Centre, Dep. Of Chemistry
University of Cambridge
CB2 1EW, UK
+44-1223-763069
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