On 01/15/2018 02:43 PM, Tim Dudgeon wrote:

> Could there be something in a more general project to bridge the
> compound (mol/smiles), sequence (protein/nucleotide seq + alignments)
> and structure (pdb/mmcif/mmtf) worlds?

FWIW PDB builds everything up from structure because they can derive
bonds from the coordinates and that's the only way you can do it in the
code. Without bonds, trying to link compounds in a sequence doesn't
really work even if you have two cysteins in a bog standard protein
sequence, with generic compounds it gets too hard fast.

PDB has in the mmCIF chem. comp. model "leaving atom flag" that marks
*a* bonding site but it doesn't tell you what kind of bond can form
there, nor what to do if there's more than one. You need a whole lot of
other code to figure out how to link two compounds into a sequence.

And then there's structure calculation that I don't know if there's
anything that works on not proteins, or can predict disordered regions
well etc.

If anyone's counting votes, pretty 2D depictions get mine.
Dimitri Maziuk
BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu

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