Search results

The Results to your search are sort by their bitterDB id. In order to get a full compound entry click on the compound id or it's name. It is possible also to download a SDF file of selected compound, check the required compounds and click on the download button in the top right of the page.

Receptor Search

To search BitterDB Receptors enter the query terms in the search box and click search. The BitterDB allows searching bitter receptors using different criteria:

Receptor Name:

Search bitter Receptors by its Gene name, Protein Name or other common name the receptor is associated with. For example, Taste receptor type 2 member 38 can be searched by the following keywords: hTAS2R38, TAS2R38, T2R38,T2R61, TAS2R61, hTAS2R61, Taste receptor type 2 member 61, PTC, PTC bitter taste receptor. This search option is implemented via the "implied Boolean logic".

Ligand Name:

Search bitter receptors by their associated ligand. For example, the results of the search term "caffeine" are five different bitter receptors. The search option is implemented via the implied Boolean logic".

UniProtKB accession number:

Search bitter receptors by their UniProtKB accession number.

This search form contains two more fields:

Has Mutation:

Search bitter Receptors which have/have not mutation data.

Has Ligands:

Search bitter Receptors which have known ligands or those that are orphan receptors.

If these fields are used with a term in the top search box they are 'ANDed' together, meaning that the receptors that are found comply with ALL the terms that were specified.

Boolean logic

• + stands for AND
• - stands for NOT
• [no operator] implies OR
• The asterisk serves as the truncation (or wildcard) operator. It should be appended to the word to be affected. Words match if they begin with the word preceding the * operator.

Click here or more information about "implied Boolean logic".

Browse BitterDB compounds

The user may use the 'Browse BitterDB Compounds' option to browse through a table with all BitterDB compounds and their properties. The compounds can be sorted by different criteria: BitterDB ID, number of associated receptors, molecular weight, logP and more, by clicking the arrows in the columns names. The search box on the top right hand side of the table enables searching for specific compounds in the compound table. The search option is implemented such, that it filters the relevant results as soon as the search term is typed. Clicking on a specific compound name opens the compound entry page.

Browse BitterDB receptors

The user may use the 'Browse BitterDB Receptors' option to browse through a table of the 25 human bitter taste receptors. For each receptor, its alternative names, the number of bitter ligands that it is known to bind and availability of mutational data, are indicated. The receptors can be sorted according to different criteria: BitterDB receptor ID, number of associated bitter ligands, receptor name and more, by clicking the arrows in the columns names. The search box on the top right hand side of the table enables searching for specific receptors. The search option is implemented such that it filters the relevant results as soon as the search term is typed. Clicking on a specific receptor name opens the receptor entry page.

Local BLAST service

BitterDB contains local BLAST service to find local similarity between the query sequence and Human Bitter Receptors. For more detailed information on what happens behind the scenes, look at this Wikipedia article.

Human Bitter taste Receptors Alignment

The Alignment contains the 25 human bitter taste receptors, it is displayed with JalView [1] which permits editing of the alignment. By right-clicking the receptor name, a new window with the BitterDB entry for this receptor opens. The alignment shows the predicted secondary structure for each receptor as predicted by TOPCONS [2]. In each trans-membrane helix X, the most conserved residue (X.50 in Ballesteros-Weinstein numbering) [3] is colored in yellow, following the assignment in Niv et el. [4] The alignment was generated by Anat Levit using the PROMALS3D webserver [5]. It was generated with 11 sequence-distinct family A GPCRs, for which a crystal structure has been solved. .

References:

1. Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J.(2009) Jalview Version 2 - a multiple sequence alignment editor and analysis workbench. Bioinformatics 25 (9) 1189-1191 doi: 10.1093/bioinformatics/btp033
2. Hennerdal A, Elofsson A (2011) Rapid membrane protein topology prediction. Bioinformatics. 27(9):1322-3. PubMedID: 21493661
3. Ballesteros J, Weinstein H (1995) Integrated methods for the construction of three- dimensional models of structure-function relations in G protein-coupled receptors. Methods Neurosci 25:366-428.
4. Brockhoff A, Behrens M, Niv MY, Meyerhof W (2010) Structural requirements of bitter taste receptor activation.(2010) Proc Natl Acad Sci U S A 107, (24), 11110-5.
5. Pei, J., B.H. Kim, and N.V. Grishin.(2008) PROMALS3D: a tool for multiple protein sequence and structure alignments. Nucleic Acids Res 36(7): p. 2295-300. PubMedID: 18287115