Example of a simulation run for the homomeric κ-OR/κ-OR system. The instantaneous velocity of lipid molecules was calculated after interpolating the motion of the corresponding head groups over 20 ns. The density of lipids with velocity within the first quartile was calculated using a Gaussian kernel (with bandwidth 5 Å) and plotted in colors (blue, high density; white low density). The location of protein molecules is indicated approximately by plotting one single isodensity contour of the protein beads obtained with the same Gaussian kernel. The location of the center of mass of helices TM1, 4 and 6 is indicated with white, gray, and black dots, respectively.
Provasi D, Boz M, Johnston J, Filizola M
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<a rel="nofollow" class="external text" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4379167/bin/pcbi.1004148.s011.mp4">S2 Movie</a> from <cite style="font-style:normal">Provasi D, Boz M, Johnston J, Filizola M (2015). "<a rel="nofollow" class="external text" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4379167">Preferred Supramolecular Organization and Dimer Interfaces of Opioid Receptors from Simulated Self-Association</a>". <i>PLOS Computational Biology</i>. <a href="https://en.wikipedia.org/wiki/Digital_object_identifier" class="extiw" title="w:Digital object identifier">DOI</a>:<a rel="nofollow" class="external text" href="https://doi.org/10.1371/journal.pcbi.1004148">10.1371/journal.pcbi.1004148</a>. <a href="https://en.wikipedia.org/wiki/PMID" class="extiw" title="w:PMID">PMID</a> <a rel="nofollow" class="external text" href="https://www.ncbi.nlm.nih.gov/pubmed/25822938">25822938</a>. <a href="https://en.wikipedia.org/wiki/PubMed_Central" class="extiw" title="w:PubMed Central">PMC</a>: <a rel="nofollow" class="external text" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4379167">4379167</a>.</cite>