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RbDe specifications

Information


Unique identifier OMICS_06402
Name RbDe
Alternative name Residue-based Diagram editor
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability No
Maintained No

Publications for Residue-based Diagram editor

RbDe citations

 (6)
call_split

Structural Mapping and Functional Characterization of Zebrafish Class B G Protein Coupled Receptor (GPCR) with Dual Ligand Selectivity towards GLP 1 and Glucagon

2016
PLoS One
PMCID: 5145181
PMID: 27930690
DOI: 10.1371/journal.pone.0167718
call_split See protocol

[…] The snake diagram of the zfGPCR (zfGLP-1R/GCGR) was based on the output of the residue-based diagram editor RbDe []. Residues are colored using the GPCRDB coloring scheme, where residues with similar physicochemical properties are colored with the same color.All 3D structures we […]

library_books

Molecular Evolutionary Characterization of a V1R Subfamily Unique to Strepsirrhine Primates

2014
Genome Biol Evol
PMCID: 3914689
PMID: 24398377
DOI: 10.1093/gbe/evu006

[…] th full ORFs for each individual. The 5′-end of the resulting fragment begins in the middle of the 2nd TM helix and terminates on the 3′-end in the 7th TM helix. We employed the visualization program RbDe () to identify and illustrate the TM, extracellular, and intracellular regions of several representative sequences from our data set. The results were cross-validated by the G protein-coupled rec […]

library_books

Cholecystokinin receptors in Atlantic salmon: molecular cloning, gene expression, and structural basis

2013
PMCID: 3841022
PMID: 24303160
DOI: 10.1002/phy2.69

[…] Putative transmembrane domains were predicted using TMHMM 2.0 server (Denmark), which is part of the Simple Modular Architecture Research Tool. Transmembrane protein 2D topology was designed using RbDe tool of Institute of computational biomedicine, Cornell University (Skrabanek et al. ).Three-dimensional models for CCK-1R and CCK-2R1/gastrin were created and viewed using Rasmol. Because the al […]

library_books

Progesterone modulation of transmembrane helix helix interactions between the α subunit of Na/K ATPase and phospholipid N methyltransferase in the oocyte plasma membrane

2010
BMC Struct Biol
PMCID: 2887865
PMID: 20500835
DOI: 10.1186/1472-6807-10-12

[…] se (PE-NMT) and the sphingomyelin (SM) synthase obtained from a variety of species. SIB BLAST searches were carried out using the BLAST network service: NCBI BLAST program reference [PMID: 9254694].A Residue-based Diagram editor (RbDe) Web site maintained by the Department of Physiology and Biophysics, Weill Medical College of Cornell University, New York, NY, was employed to illustrate the topolo […]

library_books

An evaluation of human protein protein interaction data in the public domain

2006
BMC Bioinformatics
PMCID: 1764475
PMID: 17254303
DOI: 10.1186/1471-2105-7-S5-S19

[…] ncluded in PDZBase. PDZ domains and their ligands can be queried using sequence motifs. Each interaction in PDZBase consists of the residues of the interacting proteins on a 2D-diagram generated by a residue-based-diagram-editor (RBDG). The interacting residues between the PDZ domain and their peptide ligands are predicted based on similarity with the available structures of PDZ-peptide complexes. […]

library_books

Atypical Membrane Topology and Heteromeric Function of Drosophila Odorant Receptors In Vivo

2006
PLoS Biol
PMCID: 1334387
PMID: 16402857
DOI: 10.1371/journal.pbio.0040020

[…] amily members. N-glycosylation sites were predicted using the NetNGlyc 1.0 Server (http://www.cbs.dtu.dk/services/NetNGlyc). Graphical representations of OR sequences as snake plots were adapted from Residue-based Diagram editor outputs obtained from the GPCR database []. The accession numbers of all protein sequences analyzed are available on request. […]

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RbDe institution(s)
Department of Physiology and Biophysics, Mount Sinai School of Medicine, New York, NY, USA
RbDe funding source(s)
This work was supported in part by NIH grants P01 DA124080, P20 HL69733 and the Institute for Computational Biomedicine at MSSM.

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