BO lunch meeting Tuesday?

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GNU-Darwin: Molecules and Molecule of the Day, Molecules <at> GNU-Darwin .org

We have 4 million small molecules in pdb format, with many more to
come.  Check it out.  

http://molecules.gnu-darwin.org/

Be sure and scroll down to the News block, if you are wondering what it
is about.

Regards,
Michael L. Love Ph.D
Department of Biophysics and Biophysical Chemistry
School of Medicine
Johns Hopkins University
725 N. Wolfe Street
Room 608B WBSB
Baltimore MD 21205-2185

Interoffice Mail: 608B WBSB, SoM
Shipping Dock: 1915 E. Madison St.

office: 410-614-2267
lab:    410-614-3179
fax:    410-502-6910
cell:   443-824-3451
http://www.gnu-darwin.org/

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Re: GNU-Darwin: Molecules and Molecule of the Day, Molecules <at> GNU-Darwin .org

On Thu, Aug 21, 2008 at 1:43 PM,  <proclus@...> wrote:
> We have 4 million small molecules in pdb format, with many more to
> come.  Check it out.
>
> http://molecules.gnu-darwin.org/

Might you please add some copyright/license information to those
pages? Under what conditions can these PDB files be modified,
redistributed, etc...

Egon

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Re: GNU-Darwin: Molecules and Molecule of the Day, Molecules <at> GNU-Darwin .org

On Aug 21, 2008, at 7:43 AM, proclus@... wrote:
>
> We have 4 million small molecules in pdb format, with many more to
> come.  Check it out.
>
> http://molecules.gnu-darwin.org

Where do the structures come from? Other databases?

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Re: GNU-Darwin: Molecules and Molecule of the Day, Molecules <at> GNU-Darwin .org

On Aug 21, 2008, at 7:43 AM, proclus@... wrote:
> We have 4 million small molecules in pdb format, with many more to
> come.  Check it out.

I think this is great, but I'm curious about the origins of the  
molecules and coordinates. Are you grabbing these from a database? Are  
these run through a computational package to optimize the coordinates  
in any fashion? (It's clear that they've been run through Babel-1.6,  
which isn't truly a FOSS program.)

Just like free software, it's important to know the origins of data.  
If it's derived from a closed database, it's unlikely these can really  
be freely redistributed.

Cheers,
-Geoff

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Re: GNU-Darwin: Molecules and Molecule of the Day, Molecules <at> GNU-Darwin .org

On Aug 22, 2008, at 4:43 PM, proclus@... wrote:

> It is my understanding that Babel is FOSS.  If this is incorrect,
> please be sure to let me know.

No, it is not. The original Babel (which you used) does not have any  
sort of open source license. It's free to distribute, but was blocked  
from Debian because of the license.

This is separate from Open Babel, which is true GPL. (It's also better.)
http://openbabel.org/

> beautifully.  In order to address this problem of poor geometry, we  
> plan
> to provide high quality minimized structures based on the pdb files
> that we generate.

You may find Open Babel 2.2 interesting, since it offers conformer  
searching and molecular mechanics. For drug-like molecules (i.e., no  
exotic elements), you could easily take the tools/obconformer code and  
run it over your PDB files. This will run MMFF94 conformer searching  
and geometry optimization. If you're likely to encounter more  
elements, you will probably want to try changing the force field to UFF.

You may also want to consider working with Rajarshi and Indiana about  
their Pub3D database:
http://www.chembiogrid.org/products/index.html

Cheers,
-Geoff

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Re: GNU-Darwin: Molecules and Molecule of the Day, Molecules <at> GNU-Darwin .org

There is no indication in the babel-1.6 source tree that I could find
to indicate that it is not FOSS.  It looks like openbabel-2.1.1 is in
the package tree, and it would be worth checking out I take it.  In
fact, thank you for the excellent suggestions!

Regards,

On 25 Aug, Geoffrey Hutchison wrote:
> 
> On Aug 22, 2008, at 4:43 PM, proclus@... wrote:
> 
>> It is my understanding that Babel is FOSS.  If this is incorrect,
>> please be sure to let me know.
> 
> No, it is not. The original Babel (which you used) does not have any  
> sort of open source license. It's free to distribute, but was blocked  
> from Debian because of the license.
> 
> This is separate from Open Babel, which is true GPL. (It's also better.)
> http://openbabel.org/
> 
>> beautifully.  In order to address this problem of poor geometry, we  
>> plan
>> to provide high quality minimized structures based on the pdb files
>> that we generate.
> 
> You may find Open Babel 2.2 interesting, since it offers conformer  
> searching and molecular mechanics. For drug-like molecules (i.e., no  
> exotic elements), you could easily take the tools/obconformer code and  
> run it over your PDB files. This will run MMFF94 conformer searching  
> and geometry optimization. If you're likely to encounter more  
> elements, you will probably want to try changing the force field to UFF.
> 
> You may also want to consider working with Rajarshi and Indiana about  
> their Pub3D database:
> http://www.chembiogrid.org/products/index.html
> 
> Cheers,
> -Geoff

-- 
Michael L. Love Ph.D
Department of Biophysics and Biophysical Chemistry
School of Medicine
Johns Hopkins University
725 N. Wolfe Street
Room 608B WBSB
Baltimore MD 21205-2185

Interoffice Mail: 608B WBSB, SoM

office: 410-614-2267
lab:    410-614-3179
fax:    410-502-6910
cell:   443-824-3451
http://www.gnu-darwin.org/

Visit proclus realm! http://proclus.tripod.com/
-----BEGIN GEEK CODE BLOCK-----
Version: 3.1
GMU/S d+ <at>  s: a+ C++++ UBULI++++$ P+ L+++(++++) E--- W++ N- !o K- w--- !O
M++ <at>  V-- PS+++ PE Y+ PGP-- t+++(+) 5+++ X+ R tv-(--) <at>  b !DI D- G e++++
h--- r+++ y++++
------END GEEK CODE BLOCK------

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Re: GNU-Darwin: Molecules and Molecule of the Day, Molecules <at> GNU-Darwin .org

On Aug 25, 2008, at 3:56 PM, proclus@... wrote:

> There is no indication in the babel-1.6 source tree that I could find
> to indicate that it is not FOSS.

If you take a look at any source file:
> This file is part of the Babel Program
> Copyright (C) 1992-96 W. Patrick Walters and Matthew T. Stahl
> All Rights Reserved

To me, that pretty much rules out open source.

> It looks like openbabel-2.1.1 is in the package tree, and it would  
> be worth checking out I take it.  In

I'd certainly suggest Open Babel 2.2.0. Trust me, it has a lot of  
fixes over 2.1.1. 

Cheers,
-Geoff

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Re: GNU-Darwin: Molecules and Molecule of the Day, Molecules <at> GNU-Darwin .org

On 25 Aug, Geoffrey Hutchison wrote:
> 
> On Aug 25, 2008, at 3:56 PM, proclus@... wrote:
> 
>> There is no indication in the babel-1.6 source tree that I could find
>> to indicate that it is not FOSS.
> 
> If you take a look at any source file:
>> This file is part of the Babel Program
>> Copyright (C) 1992-96 W. Patrick Walters and Matthew T. Stahl
>> All Rights Reserved

This common perception about the rights reserved clause is mistaken,
and many free software sources have such a clause.  They nonetheless
satisfy every definition of software freedom, unless the copyright
holder has stipulated some restriction, on distribution for example, or
moved to quell the inclusion of the code in other programs.  It is clear
to me from the readme file that the authors intended to encourage
downloading and redistribution, etc.

> To me, that pretty much rules out open source.
> 
>> It looks like openbabel-2.1.1 is in the package tree, and it would  
>> be worth checking out I take it.  In
> 
> I'd certainly suggest Open Babel 2.2.0. Trust me, it has a lot of  
> fixes over 2.1.1. 

Thanks again!

Regards,
Michael L. Love

> Cheers,
> -Geoff

-- 
Michael L. Love Ph.D
Department of Biophysics and Biophysical Chemistry
School of Medicine
Johns Hopkins University
725 N. Wolfe Street
Room 608B WBSB
Baltimore MD 21205-2185

Interoffice Mail: 608B WBSB, SoM

office: 410-614-2267
lab:    410-614-3179
fax:    410-502-6910
cell:   443-824-3451
http://www.gnu-darwin.org/

Visit proclus realm! http://proclus.tripod.com/
-----BEGIN GEEK CODE BLOCK-----
Version: 3.1
GMU/S d+ <at>  s: a+ C++++ UBULI++++$ P+ L+++(++++) E--- W++ N- !o K- w--- !O
M++ <at>  V-- PS+++ PE Y+ PGP-- t+++(+) 5+++ X+ R tv-(--) <at>  b !DI D- G e++++
h--- r+++ y++++
------END GEEK CODE BLOCK------

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Ubiquity

Hi, a number of people have probably already heard about Ubiquity for  
Firefox (http://labs.mozilla.com/2008/08/introducing-ubiquity/) -  
which to my mind is essentially Quicksilver for the browser. But for  
those who haven't I thought I'd post t here

In any case it's amazingly handy - while browsing a page you could  
select a piece of text and do things with it. For people on this  
list, a natural thing to do would be cheminformatics stuff.

For example, select a SMILES and view a depiction or select a  
compound name (common name, CAS RN etc) and get the SMILES for it,  
etc. I've put up two Ubiquity commands that do this at http:// 
cheminfo.informatics.indiana.edu/~rguha/code/ubiquity/

Though stuff like Greasemonkey can do (and has done) similar things -  
the "ubiquitousness" of Ubiquity is just plain cool!

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