Introducing the first in a series of videos that will explain how to use this website. Here we cover the 3D receptor model viewer and illustrate how to view a ligand docked inside a receptor.
Read MoreSilva Teixeira, Silva Ferreira, and Cerqueira (2016) identify OR3A1 as a putative receptor for some of the molecules that cause cork taint in wine. Here at primaryodors.org, OR3A1 has been assigned the green perceptual note based on it being the only known receptor for trifernal and the pure leafy green aroma of that same compound, […]
Read MoreAn error was found in the code that was measuring the types and strengths of interactions between odorants and individual binding site residues (BSRs). The gist of the error was that it treated every ligand atom as capable of only van der Waals interactions, the kind that saturated hydrocarbons have, and therefore did not calculate […]
Read MoreEarlier this year, a paper was published describing the use of machine learning (ML) to predict the activation of a human GPCR in response to ligands, based on computation of ligand binding in docking models. The authors claim up to 90% success rate. All of the human olfactory receptors are GPCRs, and computational prediction of […]
Read MoreThree receptors for allyl phenylacetate have been experimentally identified: OR1A1, OR2W1, and OR51L1. Correlation coefficients have made it possible to tentatively assign perceptual notes to these three ORs: herbal for 1A1, fresh/powdery for 2W1, and creamy for 51L1. Allyl phenylacetate itself has a honey type aroma, so it seems plausible that the honey note may […]
Read MoreSome 142 human olfactory receptors have been de-orphaned to known odorant ligands. Of these receptors, a few are highly specific in the types of odorants they respond to, while a few others are broadly tuned generalists, and the remainder fall somewhere in between these extremes. This is true not only in relation to the molecular […]
Read MoreThe challenge of writing good molecular docking code has proven immense. Through almost 5 years, each generation of code grew into a huge monster, difficult to maintain, and slow to generate results. This, compounded with the inability to devote suficient time to the endeavor due to unrelated obligations, made the task daunting. It was estimated […]
Read MoreCurrently, the intention is to develop receptor-ligand modeling that predicts as closely as possible the experimental OR-odorant data, and then extend this calculation to every combination of OR/TAAR and aroma compound in the database, in order to deorphan all the receptors and assign aroma notes to them based on their computed responses. There are 434 […]
Read MoreCurrent work for this website includes attempts to correlate A.) simulated binding parameters of odorants in receptor binding pockets to B.) experimental data from the list of references. But how internaly consistent is item B? Do the various sources report compatible information?
Read MoreIt has been proposed that the opponent process model, known to be important to color vision, might also apply to some if not all of the other senses, including olfaction. In the course of formulating my own perfumes, I have gathered a collection of essential oils (EOs), fragrance oils (FOs), and aroma compounds. Through trial […]
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