[gmx-developers] Implementation of the Hungarian Algorithm on gmx rms (former g_rms)

David van der Spoel spoel at xray.bmc.uu.se
Fri Mar 13 07:55:35 CET 2015

On 2015-03-13 00:39, João M. Damas wrote:
> Dear developers,
> I'll start by saying that I'm not requesting anything: it's not my
> intention and it's frowned upon :-)
> My intention is rather to call your attention to an algorithm that deals
> quite elegantly with symmetry issues while calculating RMSD. You can see
> here the paper with the implementation (even though the algorithm seems
> to have been developed long ago): dx.doi.org/10.1021/ci400534h
> <http://dx.doi.org/10.1021/ci400534h>
> While the advantages are quite obvious for the field of molecular
> docking and structure-based design, I think a general tool such as gmx
> rms (formerly g_rms) can benefit greatly from its implementation (they
> even discuss it in the paper).
> Recently I had to solve a symmetry problem while analysing the results
> of high-throughput MD simulations of a ligand - protein system. Luckily,
> my ligand only has planar symmetry with an inversion centre (and it was
> impossible at this time to implement the aforementioned algorithm), so I
> constructed the "symmetry mates" by scripting and calculated the RMSD
> "symmetry-corrected" matrix, which I "fed" to g_cluster. A simple
> standard RMSD vs. symmetry-corrected RMSD shows that the standard RMSD
> is overestimating the distance between a great amount of pairs of
> structures (ligand poses) due to the symmetry issue (see peak around
> [1,0.5]):
> Of course g_cluster will create non-sense clusters or wrongly attribute
> structures to clusters (I'm sorry, I cannot share those results).
> This stands just as a proof-of-concept for the importance of such
> algorithm. I'm remembering a few others, such as branching
> (bio)molecules with symmetrical branches, but I'm sure there are a lot
> more applications from this community that could benefit from such an
> implementation (as an option, not as a replacement, of course).
> Thank you for taking the time to read this.

You are more than welcome to implement this in gmx rms and upload a 
patch to gerrit.gromacs.org.

> Best regards,
> João
> --
> João M. Damas
> PhD Student
> Protein Modelling Group
> ITQB-UNL, Oeiras, Portugal
> Tel:+351-214469613 <tel:%2B351-214469613>

David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se

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