Welcome to Molecules@gnu-darwin.org
Molecule News and Molecule of the Day
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This site is under constant constructionThe molecule of the day is: Citric AcidCitric acid, also known as vitamin C is a key metabolic molecule, for which the Krebs or Citric Acid cycle was named. This molecule was made famous by the great Linus Pauling, who proposed that it might be a cure for the common cold. Although that proposal has not found very much support, the molecule does remain key and crucial. Vitamin C is able to make some other supplements and drugs more soluble, so that they are better absorbed in the digestive tract. It provides much of the exceptional tart flavor of citrus and other fruits, and like acetic acid, it has preservative qualities. It is also a part of the biochemical pathway by which cells convert the energy in carbon bonds into forms that are more useful to the cell, such as the chemical potential of ATP, and various concentration gradient potentials. Strangely, most animals naturally make far more citric acid than humans do, and one wonders if this is a good justification for supplementing the human diet with vitamin C, which is an essential vitamin. Either way, citric acid is clearly a star molecule indeed! Citric acid related molecules gallery and structural archive other names: 2-Hydroxy-1,2,3-propanetricarboxylic acid 2-Hydroxytricarballylic acid 77-92-9 C00158 Citrate Citric acid Canonical SMILES: C(C(=O)O)C(CC(=O)O)(C(=O)O)O
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 pdb file:3405.pdb directory:3405 CAS: 77-92-9
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Molecule News
updated Wed Sep 3 12:05:13 EDT 2008I have automated the process to make molecule galleries, which I am finding very useful to my research, so I thought that I would share the opportunity and take requests. It is quick and easy. I did a bisphenol search today, and as I expected, the search turned up a few stilbenes, which is the same molecular family as resveratrol. Strikingly, Bisphenol A is a noted teratogen, which shows that care must be taken when using such molecules during development. Here is a link to the bisphenol gallery.
http://molecules.gnu-darwin.org/mod/Bisphenol-more.html
If you would find it useful, I am definitely interested in taking requests for molecule galleries. Just send me the name of your favorite molecule. As you may be able to tell, we have access for galleries to about 1% or 0.5 million structures, in the total archive thus far, but it is already quite useful. The automated jobs are underway to fill in the rest. The next milestone is the capability to index and make galleries for the remaining millions of molecules for which we have pdb files already, which would be 5-10% complete. Any comments or suggestions are also welcome.
A terminal screenshot has been added to the right sidebar, in order to show the kind of code that is being used to generate the Molecules directory indices. All inquiries and suggestions are welcome.
updated Fri Aug 29 14:39:14 EDT 2008
Reaction to our website has been quite positive and encouraging, but people are anxious to see structures with improved stereochemistry. We have received many suggestions about how to make that happen faster. For the time being, we are experiencing the best structure viewing results with RasMOL. Name extraction and structure file linking jobs are underway, which is an indication that we are still in a preliminary phase. Google spiders more almost everyday, and past experience indicates that the search capability will become very useful indeed! Here is some secret mumbo jumbo. I'm afraid that my Japanese or Korean is broken at best ;-}. Enjoy!
updated Wed Aug 27 21:38:32 EDT 2008
An RSS News Feed has been added to the right side bar.
updated Tue Aug 26 19:27:29 EDT 2008
Several new indices have been added to our sidebar, notably; current index by name, and gallery by name. These are large indices, but also vastly incomplete, and work is underway to improve them. A list of bloggers who have mentioned the site, with links in their blogs, is now in the front sidebar, although only one is known thus far. Due to the vastness of the scale, many of these things will be divided out and buried a little deeper eventually, but they can be showcased now, and they are a good survey.
updated Tue Aug 19 19:45:09 EDT 2008
Some facts: The Molecules website contains more than 4 million small molecule structure files in pdb format, and molecular graphics representations. About 50 million molecules are still in the pipe, and they are expected to appear here over the course of the next few weeks and months. The pdb format is readable by common FOSS molecule viewer software, such as RasMol and PyMOL. In due course, we plan to provide high quality structures via energy minimization refinement, and additional resources.
Molecules@gnu-darwin.org is founded in the spirit of free software, open source, and public access. It is hoped that access to these files will be a wonderful community resource for science education, research, and entertainment as well. We are looking for investment, funding, or sponsorship in order to expedite and expand this work, and lead the field, with an eye towards an advanced, complete, synthetic, structural, and informatical bioorganome. Meanwhile, the site is already an exceptional lab resource, and molecular catalog, providing the means and building blocks towards additional novel structures. We aim to be the best.
The structural biology, protein crystallography, and molecular graphics talent that is building the Molecules archive is available to work for you in a contract or consulting arrangement. Wide-ranging expertise is available. Molecules@gnu-darwin.org is built entirely with FOSS, free and open source software, GNU-Darwin OS, and it is under the aegis of The GNU-Darwin Distribution. Here is a link to the Distribution résumé. Our founder is an X-ray laboratory admin for the Department of Biophysics and Biophysical Chemistry of Johns Hopkins University School of Medicine. You can also read his CV. We would like to build a community around this website, and we are looking for volunteers and collaborators to help. Regarding any aspect of the work of this site, please feel free to contact us, molecules@gnu-darwin.org, with gdmolecules in the subject line. Cheers!