For purposes of researching more accurate computation and prediction of receptor-ligand interactions and receptor activation by agonists, we have created a molecular docker. Like other software packages such as AutoDock and LeDock, our application finds ligand conformers (poses) inside binding pockets of proteins and is available free of charge. But in addition, POdock outputs not […]
Read MoreThe author is unusually sensitive to myrac aldehyde (also known as Empetal) and perceives in it an intense milky aroma. Other individuals do not seem to share this perception, or at least not to the same degree. Myrac aldehyde is a precursor to the production of lyral, and the two molecules differ very little in […]
Read MoreThere’s a perceptual aroma note, common to such aroma characters as berry, wine, grape, plum, geranium, anise, and clove, that can only be described as “purple”. It appears to make up part of the two candidate primaries referred to on this website as jammy and xyloenanthic. “Purple” smelling aroma molecules are disproportionately associated with the […]
Read MoreThe agonist mixtures for OR2W1 reveal a perceptual note best described as “stale”, that seems to be enhanced by the presence of OR1A1 agonists or OR2J2 agonists. 2W1 is highly sensitive to geraniol and citronellol, both of which have a certain fetid-vegetable note that’s very noticeable in the aromas of geranium oil and citronella oil, […]
Read MoreSubjects with two copies of a mutated version of the OR5A1 receptor report the smell of β-ionone as vinegar-like instead of floral. The overall sensitivity to this compound is also reduced. We have used these facts to assign the floral perceptual note to OR5A1. However, the mutation is at position 183 in one of the […]
Read MoreOR5A1 has one known agonist, β-ionone, which has a distinctive floral violet tart dry woody fruity berry aroma. By itself, this would not be enough information to assign one aroma note to the receptor, but it has been found that a polymorphism on the OR5A1 gene causes individuals with two variant copies to perceive β-ionone […]
Read MoreTo characterize the contributions of single olfactory receptors (ORs) to the perception of aromas, mixtures were prepared of agonists for individual ORs and smelled. The hypothesis is that the various aroma chemicals will dilute each other’s effect on ORs other than the target receptor, leaving a mixture that smells mostly like the target receptor’s contribution. […]
Read MoreFloralozone is one of several aroma compounds that evoke a perception known as “aquatic”, “watery”, “ozone”, “muguet”, “rhubarb”, etc. Other compounds that evoke such a perceptual note include cyclamen aldehyde, calone (watermelon ketone), lyral, bourgeonal, lilial, 1-decanol, and 1-dodecanol. Some of the strongest agonists of OR1D2 have this note, though not all OR1D2 agonists do. […]
Read MoreOlfactory receptors (ORs), being G-protein coupled receptors (GPCRs), exist in an equilibrium between several conformational states. Most of the time, the dominant conformation is the inactive state, which cannot bind a G-protein and signal the cell to the presence of an odorant, while a certain other conformation can bind a G-protein and initiate this signaling, […]
Read MoreAccording to an article by Cheng et al (2010), figure 1, there exist several pathways for GPCR signaling following receptor activation. One of these involves cAMP while another involves Ca²⁺. However, there is the potential for false positives by this method, as well as false negatives because a given receptor or receptor-ligand pair might bind […]
Read More