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Molecule News Go straight to site news Molecule of the Day Archive(MOD) Archive Links alphanumeric index sdf archives numeric index pdb files by numeric sdf files by numeric current index by name gallery by name Developer Links infrastructure hardware and package set Search warning: not yet fully spidered Enter your search terms Molecules Web Submit search form Blogged by: Antony Williams Gavin Baker (Peter Suber)

This site is under constant construction The molecule of the day is: Fructose Fructose is a key molecule in the metabolic pathways of the cell, and it is also a very sweet sugar, which gives many fruits their characteristic sweetness. The fructose molecule provides much of the metabolic energy to the cell, but it is likely that it bears a lower glycemic load than other sugars, such as glucose and sucrose. This could be one reason why fruit is better for you than soda drinks! I get mine in a juice concentrate, which is also much less expensive than soda. Fructose rocks! Fructose related molecules gallery and structural archive other names: 57-48-7 C00095 D-Fructose D-arabino-Hexulose Fruit sugar Levulose Canonical SMILES: C(C1C(C(C(O1)(CO)O)O)O)O related molecule names: 57-48-7 C10906 D-Fructose Amino-D-fructose 6-phosphate Aminofructose 6-phosphate C12214 CPD-535 D-Fructose 2,6-bisphosphate DEOXYMORPHOLINOFRUCTOSE 30237-26-4 D-fructose D-fructose-ring FRU fru-ring fructose fructosteril laevoral laevosan levugen levulose 15978-08-2 D-fructose-1-phosphate FRU1P beta-D-fructose-1-P beta-D-fructose-1-phosphate fructose-1-P fructose-1-phosphate 488-69-7 D-Fructose 1,6-bis(dihydrogenphosphate) D-fructose-1,6-bisphosphate D-fructose-1,6-diphosphate FRUCTOSE-16-DIPHOSPHATE alpha-D-fructose-1,6-diphosphate fructose-1,6-bisphosphate fructose-1,6-diphosphate 643-13-0 A-D-fructose-6-P D-fructose-6-P D-fructose-6-phosphate FRUCTOSE-6P fru-6-P fruc6p fructose-6-P fructose-6-phosphate FRUCTOSEGLYCINE FRUCTOSELYSINE FRUCTOSELYSINE-6-PHOSPHATE fructoselysine-6-P 643-13-0 C00085 D-Fructose 6-phosphate D-Fructose 6-phosphoric acid Neuberg ester 57-48-7 C00095 D-Fructose D-arabino-Hexulose Fruit sugar Levulose 5-Dehydro-D-fructose C00273 488-69-7 C00354 D-Fructose 1,6-bisphosphate C00665 D-Fructose 2,6-bisphosphate beta-D-Fructose 2,6-bisphosphate 15978-08-2 C01094 D-Fructose 1-phosphate C01496 Fructose arabino-Hexulose 7776-48-9 C01719 L-Fructose L-arabino-Hexulose 53188-23-1 C02336 Fructose beta-D-Fructose beta-D-arabino-Hexulose beta-Fruit sugar beta-Levulose C02976 Fructose 1-phosphate C03267 beta-D-Fructofuranose 2-phosphate beta-D-Fructose 2-phosphate Bis-D-fructose 2',1:2,1'-dianhydride C04333 C05000 Fructose 1-phosphate(furanose) C05001 Fructose 1-phosphate(pyranose) C05003 Fructose(pyranose) C05345 beta-D-Fructose 6-phosphate C05378 beta-D-Fructose 1,6-bisphosphate 551-68-8 C06468 D-Allulose D-Altrulose D-Pseudofructose D-Psicose D-erythro-Hexulose D-ribo-2-Hexulose D-ribo-2-Ketohexulose 1,5-Anhydro-D-fructose C06485 512-72-1 Ajugose C08238 alpha-Galactosyl-(1-6)-alpha-galactosyl-(1-6)-alpha-galactosyl-(1-6)-alpha-galactosyl-(1-6)-alpha-glucosyl-(1-2)-beta-fructose 547-25-1 D-(+)-Turanose D-Fructose, 3-O-.alpha.-D-glucopyranosyl- D-Turanose NSC1222 TURANOSE 534-97-4 D-Fructosazone D-Fructose phenylosazone D-Glucosazone D-Glucose phenylosazone D-Mannosazone D-Mannose phenylosazone D-arabino-Hexos-2-ulose, bis(phenylhydrazone) D-arabino-Hexosulose, bis(phenylhydrazone) Dextrosazone NSC2027 6347-01-9 FRUCTOSE, (D) Laevuflex NSC9250 6341-07-7 D-Fructose, 1,3,4,5,6-pentaacetate Fructose, 1,3,4,5,6-pentaacetate, D- NSC46395 D-Fructofuranosylamine, 1-deoxy-1-[(4-methylphenyl)amino]-N-(phenylmethylene)- D-Fructose, 2-benzylideneamino-1,2-dideoxy-1-p-toluidino- NSC47582 .alpha.-D-Fructofuranose 1,6-diphosphate .alpha.-D-Fructofuranose, 1,6-bis(dihydrogen phosphate) 34693-23-7 FRUCTOSE,L,6-DIPHOSPHASE NSC57553 10597-68-9 196419-06-4 3812-57-5 57-48-7 69-67-0 AI3-23514 CCRIS 3335 D-(-)-Fructose D-(-)-Levulose D-Fructose EINECS 200-333-3 FRUCTOSE Fructose [JAN] Fructose solution Fructose, D- Fructose, pure Fruit sugar Furucton Hi-Fructo 970 Krystar 300 Levulose Nevulose Sugar, fruit arabino-Hexulose 125740-83-2 15499-52-2 23558-08-9 23784-19-2 26177-85-5 34378-77-3 38099-82-0 4004-40-4 488-69-7 6035-52-5 6055-82-9 77-82-7 D-Fructofuranose, 1,6-bis(dihydrogen phosphate) D-Fructose, 1,6-bis(dihydrogen phosphate) D-Fructose-1,6-bis(dihydrogenphosphat) D-arabino-2-Hexulose-1,6-bis(dihydrogenphosphat) EINECS 207-683-6 ESAFOSFINA Fructose-1,6-bisphosphate Fructose-1,6-diphosphate Harden-Young-Ester 4429-04-3 D-Fructose, 1-amino-1-deoxy- D-Isoglucosamine FRUCTOSAMINE

pdb file:3342.pdb directory:3342 CAS: 57-48-7 MOD screenshot MOD termshot RSS News Feed (syndicate freely:)

Molecule News

Added developer links to the left side bar.

updated Wed Sep 3 12:05:13 EDT 2008

I 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 pregnancy, nursing, and 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.

updated Tue Sep 2 14:10:15 EDT 2008

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!

• & , .61,800 .620,000¬ 04¼ 1 25¼ ¬ ¬ µ¤! ­ ° ± µ¤. ¼´ ±  ´ *

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!