Integrating Heterogeneous Odor Response Data into a Common Response Model: A DoOR to the Complete Olfactome

Galizia, C. Giovanni; Münch, Daniel; Strauch, Martin; Nissler, Anja; Ma, Shouwen

doi:10.1093/chemse/bjq042

Cited by 97 publications

(107 citation statements)

References 34 publications

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“…We take the neural data of DoOR database [47] and we calculate molecular volume (supplemental file 3) using a computational chemistry software -VEGA ZZ [61]. We used GNU R to analyse the data [62].…”

Section: Methodsmentioning

confidence: 99%

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Olfactory receptors are sensitive to molecular volume of odorants

Saberi

Seyed-allaei

2015

Preprint

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To study olfaction, first we should know which physical or chemical properties of odorant molecules determine the response of olfactory receptor neurons, and then we should study the effect of those properties on the combinatorial encoding in olfactory system.In this work we show that the response of an olfactory receptor neuron in Drosophila depends on molecular volume of an odorant; The molecular volume determines the upper limits of the neural response, while the actual neural response may depend on other properties of the molecules. Each olfactory receptor prefers a particular volume, with some degree of flexibility. These two parameters predict the volume and flexibility of the binding-pocket of the olfactory receptors, which are the targets of structural biology studies.At the end we argue that the molecular volume can affects the quality of perceived smell of an odorant via the combinatorial encoding, molecular volume may mask other underlying relations between properties of molecules and neural responses and we suggest a way to improve the selection of odorants in further experimental studies.

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Section: Methodsmentioning

confidence: 99%

“…http://dx.doi.org/10.1101/013516 doi: bioRxiv preprint first posted online Jan. 6, 2015; -DoOR -that includes the neural responses of most olfactory receptors (OR) of Drosophila to many odorants [47]. This database has collected its data from many other sources [18,20,[48][49][50][51][52][53][54][55][56][57][58][59][60].…”

Section: Introductionmentioning

confidence: 99%

Olfactory receptors are sensitive to molecular volume of odorants

Saberi

Seyed-allaei

2015

Preprint

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“…As input to our network we used a subset of the DoOR odorant response database [11]. In this database each odorant is represented as an ORN activation vector of mean-rate activity.…”

Section: Methodsmentioning

confidence: 99%

Exploring olfactory sensory networks: Simulations and hardware emulation

Beyeler

Proske

Galizia

et al. 2010

2010 Biomedical Circuits and Systems Conference (BioCAS)

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Abstract-Olfactory stimuli are represented in a highdimensional space by neural networks of the olfactory system. A great deal of research in olfaction has focused on this representation within the first processing stage, the olfactory bulb (vertebrates) or antennal lobe (insects) glomeruli. In particular the mapping of chemical stimuli onto olfactory glomeruli and the relation of this mapping to perceptual qualities have been investigated. While a number of studies have illustrated the importance of inhibitory networks within the olfactory bulb or the antennal lobe for the shaping and processing of olfactory information, it is not clear how exactly these inhibitory networks are organized to provide filtering and contrast enhancement capabilities. In this work the aim is to study the topology of the proposed networks by using software simulations and hardware implementation. While we can study the dependence of the activity on each parameter of the theoretical models with the simulations, it is important to understand whether the models can be used in robotic applications for real-time odor recognition. We present the results of a linear simulation, a spiking simulation with I&F neurons and a real-time hardware emulation using neuromorphic VLSI chips. We used an input data set of neurophysiological recordings from olfactory receptive neurons of insects, especially Drosophila.

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“…In SuperScent, SuperSweet and BitterDB some of the data on each molecule can be downloaded separately. In SSFA-GPHR the search results as 2D Snake plot or 3D homology model can be downloaded Several specialized databases are devoted to sensory receptors, including OdorDB, Olfactory Receptor Database (ORDB) (Crasto et al 2002(Crasto et al , 2003, Database of Odor Responses (DoOR) (Galizia et al 2010), ODORactor (Liu et al 2011), The Human Olfactory Data Explorer (HORDE) database (Olender et al 2004;Safran et al 2003) SuperScent (Dunkel et al 2009), SuperSweet (Ahmed et al 2011) and BitterDB (Wiener et al 2012).…”

Section: Ligand Interactions Of Particular Gpcr Familiesmentioning

confidence: 99%

GPCR & Company: Databases and Servers for GPCRs and Interacting Partners

Kowalsman

Niv

2013

Advances in Experimental Medicine and Biology

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G-protein-coupled receptors (GPCRs) are a large superfamily of membrane receptors that are involved in a wide range of signaling pathways. To fulfill their tasks, GPCRs interact with a variety of partners, including small molecules, lipids and proteins. They are accompanied by different proteins during all phases of their life cycle. Therefore, GPCR interactions with their partners are of great interest in basic cell-signaling research and in drug discovery.Due to the rapid development of computers and internet communication, knowledge and data can be easily shared within the worldwide research community via freely available databases and servers. These provide an abundance of biological, chemical and pharmacological information.This chapter describes the available web resources for investigating GPCR interactions. We review about 40 freely available databases and servers, and provide a few sentences about the essence and the data they supply. For simplification, the databases and servers were grouped under the following topics: general GPCR-ligand interactions; particular families of GPCRs and their ligands; GPCR oligomerization; GPCR interactions with intracellular partners; and structural information on GPCRs. In conclusion, a multitude of useful tools are currently available. Summary tables are provided to ease navigation between the numerous and partially overlapping resources. Suggestions for future enhancements of the online tools include the addition of links from general to specialized databases and enabling usage of user-supplied template for GPCR structural modeling.

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Integrating Heterogeneous Odor Response Data into a Common Response Model: A DoOR to the Complete Olfactome

Cited by 97 publications

References 34 publications

Olfactory receptors are sensitive to molecular volume of odorants

Olfactory receptors are sensitive to molecular volume of odorants

Exploring olfactory sensory networks: Simulations and hardware emulation

GPCR & Company: Databases and Servers for GPCRs and Interacting Partners

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