<div dir="ltr">Dear developers,<div><br></div><div>I'll start by saying that I'm not requesting anything: it's not my intention and it's frowned upon :-)</div><div><br></div><div>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): <a href="http://dx.doi.org/10.1021/ci400534h" target="_blank">dx.doi.org/10.1021/ci400534h</a></div><div><br></div><div>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).</div><div><br></div><div>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]):</div><div><br></div><div><img src="https://photos-5.dropbox.com/t/2/AADMSz7zzsmcMxUtk8iozhGUfu9W7BaUHLKF6SnmmC-2YA/12/3111184/png/1024x768/2/_/0/4/plot_nosymm-vs-symm.png/CJDyvQEgASACIAMoASgC/26omatoldwxkrh6/AACZ4DHYlW_ioeavFUEC6sUra/plot_nosymm-vs-symm.png" width="454" height="206"></div><div>Of course g_cluster will create non-sense clusters or wrongly attribute structures to clusters (I'm sorry, I cannot share those results).</div><div><br></div><div>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).<br><br></div>Thank you for taking the time to read this.<div><br></div><div>Best regards,<br></div><div>João</div><div><div><br></div>-- <br><div>João M. Damas<br>PhD Student<br>Protein Modelling Group<br>ITQB-UNL, Oeiras, Portugal<br>Tel:<a href="tel:%2B351-214469613" value="+351214469613" target="_blank">+351-214469613</a></div>
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