On 01/16/2018 06:43 AM, Dimitri Maziuk wrote:
> 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.
Chimera can do the PDB to MOL2 conversion (so there might be some
code to look at since UCSF Chimera is open source).
If you want their algorithm, I think it is in there:
@article {JCC:JCC540120716,
author = {Meng, Elaine C. and Lewis, Richard A.},
title = {Determination of molecular topology and atomic hybridization
states from heavy atom coordinates},
journal = {Journal of Computational Chemistry},
volume = {12},
number = {7},
publisher = {John Wiley & Sons, Inc.},
issn = {1096-987X},
url = {http://dx.doi.org/10.1002/jcc.540120716},
doi = {10.1002/jcc.540120716},
pages = {891--898},
year = {1991},
}
> 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.
>
>
>
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