Depth-First: Small Molecule 3D Coordinates From PubChem

Small Molecule 3D Coordinates From PubChem

Rich Apodaca — Fri, 23 May 2008 10:53:00 +0000

The PubChem team has quietly introduced a new feature - 3D coordinates for many of the small molecules in its compound collection. To my knowledge, these coordinates are only currently available via FTP. From the README:

The data contained here consists of a theoretical 3D description of PubChem Compound records computed using the MMFF94s force field without coulombic terms, including MMFF charges. Each provided theoretical 3D conformer is not a stationary point on the hyper-potential surface (i.e., is not at a minimum energy). Rather, the theoretical 3D description is a low energy conformer selected from a conformer model (a theoretical description of the conformational flexibility of a chemical structure consisting of multiple 3D representations or poses sampled using an RMSD {root mean squared distance} threshold) describing energetically-accessible and (potentially) biologically relevant coformations of a chemical structure.

Not every PubChem Compound record will have a theoretical 3D description. Structures considered too large (containing more than 50 non-hydrogen atoms) or too flexible (containing more than 15 rotatable bonds) are excluded. Furthermore, chemical structures containing elements other than H, C, N, O, F, P, S, Cl, Br, and I are also excluded.

Generation of theoretical 3D descriptions of small molecules is computationally intensive. As such, some PubChem Compound records may be added at a later time.

(A few open source packages for generating 3D conformers are also available.)

Recently, Geoff Hutchison wrote in to suggest that a potentially useful new feature of Chempedia could be the ability to directly obtain 3D coordinates for a molecule of interest.

One very economical way to do that would be to use PubChem's 3D dataset. It would also be trivial to display these coordinates as a resizable Jmol applet, in analogy to Chempedia's recently-added 2D molecule resizing feature.

Of course, there are many other potential uses for the PubChem conformer dataset, especially when applied to Web applications.

"Small Molecule 3D Coordinates From PubChem" by baoilleach

Sun, 25 May 2008 17:42:47 +0000

Soaring, all programs rely on users to report bugs. I will forward your bug report to the authors...

"Small Molecule 3D Coordinates From PubChem" by Rich Apodaca

Sat, 24 May 2008 13:45:32 +0000

Soaring, that's a disadvantage of a userscript - if something about a site changes that the script depends on, then the script breaks.

The Jmol applet is open source and has been available for some time.

"Small Molecule 3D Coordinates From PubChem" by Soaring Bear

Sat, 24 May 2008 12:54:00 +0000

Until a week or two ago when NLM changed the pubchem results layout (unannounced) there was a very nice firefox plugin that displayed 3-D structures right from the pubchem results page.
http://blueobelisk.sourceforge.net/wiki/Userscripts#Add3D_structuresto_PubChem I wish I could find out if this plugin will be patched to work with the changes? I wonder if this jMol applet James refers to will be made available?

"Small Molecule 3D Coordinates From PubChem" by James

Fri, 23 May 2008 12:42:50 +0000

Great lead. I implemented a jMol applet in one of our lab's in-house structure databases and the users have been very enthusiastic. For the effort it took, the payoff has been quite good.