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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) MOD Links Alanine Alanine-more Luteolin-more Lipoic-more Carnosine-more Salidroside-more Benfotiamine-more Fructose Fructose-more Proline-more Cyanidin-more Deoxycholate-more Stilbene-more isothiocyanate-more Bisphenol-more Citric-acid atp GNU-Darwin Links GNU-Darwin Package set of Molecules Machine Molecules@GNU-Darwin.org GNU-Darwin User Guide and Cookbook FSF: Why free software and Apple's iPhone don't mix GNU-Darwin source code repository GNU-Darwin Program Documentation Project GNU-Darwin: an attack on Iran

This site is under constant construction The molecule of the day is: Alanine Alanine is notable as a small amino acid, which is a component of protein. Due to the small size of its single methyl side chain, it is able to pack into crevices in protein structure, so that the main chains lay close together. As a result of its smallness, the protein chain is somewhat more flexible near alanine, but not as flexible as near glycine, which has no sidechain at all. Alanine related molecules gallery and structural archive other names: 56-41-7 C00041 L-2-Aminopropionic acid L-Alanine L-alpha-Alanine Canonical SMILES: CC(C(=O)O)N related molecule names: 50906-85-9 Atalanine C10644 51-65-0 C11217 p-Fluorophenylalanine 65929-03-5 C11221 FMLP OMe Formylmethionyl-leucyl-phenylalanine methyl ester 20874-31-1 C11341 N-Acetyl-DL-phenylalanine beta-naphthyl ester N-Acetylphenylalanine beta-naphthyl ester 10109-05-4 C11345 Triazolealanine 59880-97-6 C11596 FMLP N-Formyl-L-methionyl-L-leucyl-L-phenylalanine 3131-03-1 4-[4-(Dimethylamino)-N-methyl-L-phenylalanine]virginiamycin S1 C11615 Mikamycin B Pristinamycin IA Vernamycin B alpha 4-[N-Methyl-4-(methylamino)-L-phenylalanine]virginiamycin S1 57206-54-9 C11616 Pristinamycin IB Vernamycin B beta 2-D-Alanine-4-[4-(dimethylamino)-N-methyl-L-phenylalanine]virginiamycin S1 28979-74-0 C11617 Pristinamycin IC Vernamycin B gamma 2410-24-4 C12033 p-Aminophenylalanine 3-CHLORO-D-ALANINE 3-HYDROXY-L-KYNURENINE 3-hydroxy-kynurenine 606-14-4 Alanine, 3-(3-hydroxyanthraniloyl)-, L- 1115-65-7 3-SULFINOALANINE 3-Sulfino-L-alanine 3-sulphino-L-alanine L-Cysteinesulfinic acid 3-UREIDO-PROPIONATE 3-Ureidopropanoate 3-ureidopropionate N-Carbamoyl-beta-alanine beta-Ureidopropionic acid 107-95-9 3-aminopropanoate B-ALANINE beta-alanine C1 UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-6-carboxy-L-lysyl-D-alanyl-D-alanine UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminoheptanedioate- D-alanyl-D-alanine UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine C3 UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-L-lysyl-D-alanyl-D-alanine C4 N-acetylmuramoyl-L-alanyl-D-glutamyl-L-lysyl- D-alanyl-D-alanine-diphosphoundecaprenol C5 N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminoheptane- D-alanyl-D-alanine-diphosphoundecaprenol lipid intermediate I undecaprenyl-pyrophosphoryl-MurNAc-pentapeptide C6 N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminoheptane-D-alanyl-D-alanine-diphosphoundecaprenyl-N-acetylglucosamine lipid intermediate II undecaprenyl-pyrophosphoryl-MurNAc-(pentapeptide)-N-acetylglucosamine 923-16-0 D-ALA-D-ALA D-alanyl-D-alanine 338-69-2 D-ALANINE (S)-alpha-amino-1H-imidazole-4-propanoic acid 7006-35-1 71-00-1 HIS L-histidine alpha-amino-4-imidazoleproprionic acid glyoxaline-5-alanine histidine 56-41-7 6898-94-8 L-alanine L-alpha-alanine alanine 3,4-dihydroxy-L-phenylalanine 59-92-7 Dopa L-DIHYDROXY-PHENYLALANINE alanine, 3-(3,4-dihydroxyphenyl)-, L- dihydroxyphenylalanine 3,3'5-Triiodo-L-thyronine 3,5,3'-L-Triiodo-L-thyronine 3,5,3'-triiodothyronine 4-(3-iodo-4-hydroxy-phenoxy)-3,5-diiodophenylalanine 6893-02-3 L-3,5,3'-Triiodothyronine L-triiodothyronine LIOTHYRONINE O-(4-hydroxy-3-iodo-phenyl)-3,5-diiodo-L-tyrosine triiodothyronine triothyrone (R)-pantothenate 79-83-4 D-pantothenic acid PANTOTHENATE beta-alanine, (R)-N-(2,4-dihydroxy-3,3-dimethyl-oxobutyl)- pantothenic acid vitamin B5 3617-44-5 63-91-2 L-phenylalanine PHE endophenyl phenylalanine 17528-72-2 4(1H)-pteridinone, 2-amino-6-(1,2-dihydroxypropyl)-5,6,7,8-tetrahydro- 5,6,7,8-erythro-tetrahydrobiopterin 5,6,7,8-tetra-H-biopterin 5,6,7,8-tetrahydrobiopterin TETRA-H-BIOPTERIN phenylalanine hydroxylase cofactor tetra-hydro-biopterin tetrahydrobiopterin UDP-ACETYLMURAMOYL-ALA UDP-N-acetylmuramoyl-L-alanine UDP-MURNAC-TETRAPEPTIDE UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminoheptanedioate-D-alanine uridine 5'-pyrophosphoryl N-acetylmuramyl-tetrapeptide 56-41-7 C00041 L-2-Aminopropionic acid L-Alanine L-alpha-Alanine 56-45-1 C00065 L-2-Amino-3-hydroxypropionic acid L-3-Hydroxy-alanine L-Serine (S)-alpha-Amino-beta-phenylpropionic acid 63-91-2 C00079 L-Phenylalanine (S)-2-Amino-3-(p-hydroxyphenyl)propionic acid (S)-3-(p-Hydroxyphenyl)alanine 60-18-4 C00082 L-Tyrosine 107-95-9 3-Aminopropanoate 3-Aminopropionic acid C00099 beta-Alanine 338-69-2 C00133 D-2-Aminopropionic acid D-Ala D-Alanine 3-Anthraniloyl-L-alanine 343-65-7 C00328 L-Kynurenine 3,4-Dihydroxy-L-phenylalanine 3-Hydroxy-L-tyrosine 59-92-7 C00355 Dihydroxy-L-phenylalanine L-Dopa L-beta-(3,4-Dihydroxyphenyl)alanine Levodopa 13100-82-8 2-Amino-3-sulfopropionic acid 3-Sulfoalanine C00506 L-Cysteate L-Cysteic acid

pdb file:3290.pdb directory:3290 CAS: 57-48-7 MOD screenshot MOD termshot RSS News Feed (syndicate freely:)

Molecule News

Added quick navigation links to the left side bar. The site has reached 111 GB, and a massive backup is underway. We are still just getting started.

updated Thu Sep 4 13:30:20 EDT 2008

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!