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Protocols

BitterDB specifications

Information


Unique identifier OMICS_20925
Name BitterDB
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Allowed
Version 1.3
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/BitterDB

Maintainer


  • person_outline Masha Niv

Publications for BitterDB

BitterDB citations

 (5)
library_books

e Bitter: Bitterant Prediction by the Consensus Voting From the Machine Learning Methods

2018
PMCID: 5885771
PMID: 29651416
DOI: 10.3389/fchem.2018.00082

[…] rs (Huang et al., ). In their study, the dataset is composed of 539 bitterants and 539 non-bitterants. Five hundred thirty-nine bitterrants are gathered from the literature and the publicly available BitterDB (Wiener et al., ). For 539 non-bitterants, 20 non-bitterants are from their in-house bitterless compounds validated by the experiments, and 519 non-bitterants are the representative structure […]

call_split

Molecular Features Underlying Selectivity in Chicken Bitter Taste Receptors

2018
Front Mol Biosci
PMCID: 5797744
PMID: 29445727
DOI: 10.3389/fmolb.2018.00006
call_split See protocol

[…] BitterDB compounds were prepared with LigPrep (version 3.6, Schrödinger, LLC, New York, NY, 2015) through the generation of stereoisomers and protonation states at pH 7 ± 0.5 and then with Phase (vers […]

call_split

Bitter or not? BitterPredict, a tool for predicting taste from chemical structure

2017
Sci Rep
PMCID: 5608695
PMID: 28935887
DOI: 10.1038/s41598-017-12359-7
call_split See protocol

[…] Training and test sets generated and/or analysed in the current study are available from the corresponding author upon reasonable request.Matlab code for BitterPredict is provided via BitterDB http://bitterdb.agri.huji.ac.il/dbbitter.php#BitterPredict and via GitHub repository https://github.com/Niv-Lab/BitterPredict1. The allowed input is CSV or Excel file holding QikProp and phys […]

call_split

Ligand binding modes from low resolution GPCR models and mutagenesis: chicken bitter taste receptor as a test case

2017
Sci Rep
PMCID: 5557796
PMID: 28811548
DOI: 10.1038/s41598-017-08344-9
call_split See protocol

[…] chloroquin, chloramphenicol, and coumarin were analyzed as ggTas2r1 agonists. The 3D molecular structures of these compounds were downloaded from the publicly accessible electronic database, chicken BitterDB (http://bitterdb/dbbitter.php?mode_organism=Chicken), and prepared (through the generation of stereoisomers and protonation states at pH 7 ± 0.5) with LigPrep (version 3.6, Schrödinger, LLC, […]

library_books

Expanding the fragrance chemical space for virtual screening

2014
J Cheminform
PMCID: 4037718
PMID: 24876890
DOI: 10.1186/1758-2946-6-27

[…] as used. Both datasets were combined and checked for duplicates to a final list of 1760 fragrance molecule structures. For TasteDB structure representations were retrieved from the browsing option of BitterDB [] and from the Sweet-tree of SuperSweet []. Both datasets were combined and checked for duplicates to a final list of 806 taste structures. […]

Citations

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BitterDB institution(s)
The Institute of Biochemistry, Food Science and Nutrition, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel; Fritz Haber Center for Molecular Dynamics, The Hebrew University of Jerusalem, Israel
BitterDB funding source(s)
Supported by Niedersachsen-Israel Research cooperation fund and BSF grant number 2007296.

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