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Information


Unique identifier OMICS_07081
Name DoBo
Alternative name Domain Boundary
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Publication for Domain Boundary

DoBo citations

 (7)
library_books

A Fast Alignment Free Approach for De Novo Detection of Protein Conserved Regions

2016
PLoS One
PMCID: 4995020
PMID: 27552220
DOI: 10.1371/journal.pone.0161338

[…] on target is then used to find the final partitioning for each sequence. Unification is performed to construct a new graph based on final partitions and to cluster similar proteins together. In ADDA, domain boundary assessments are performed using the trees of putative domains. However, the final goal being domain family enumeration, unification is a crucial step and can possibly improve the parti […]

library_books

Roles of the novel coiled coil protein Rng10 in septum formation during fission yeast cytokinesis

2016
Mol Biol Cell
PMCID: 4985255
PMID: 27385337
DOI: 10.1091/mbc.E16-03-0156

[…] the N-terminus, Rng10 contained no other recognizable domains (). We constructed Rng10 N- and C-terminal truncations () with either mECitrine or mEGFP tag under rng10 promoter based on the predicted domain boundary () and compared their localization and intensity to those of full-length (FL) Rng10 (). Both the N- and C-terminal truncations still localized to the division site (). We measured abso […]

call_split

Extending Protein Domain Boundary Predictors to Detect Discontinuous Domains

2015
PLoS One
PMCID: 4621036
PMID: 26502173
DOI: 10.1371/journal.pone.0141541
call_split See protocol

[…] ” if the predicted boundaries are within ±20 residues away from the true boundary. Then the maximum error of a correctly predicted segment is 40 residues and these domain predictors cannot report the domain boundary when the protein domain is less than 40 residues according to this criterion.From the segment assemblies, we randomly selected 229 positive and 548 negative samples which are used as t […]

library_books

Serum Albumin Domain Structures in Human Blood Serum by Mass Spectrometry and Computational Biology*

2015
PMCID: 4813692
PMID: 26385339
DOI: 10.1074/mcp.M115.048504

[…] To demonstrate the feasibility of our combined CLMS/search approach, we decided to split HSA into smaller domains more suitable for state-of-the-art protocols. We employed the following computational domain boundary prediction methods: DoBo (), Threadom () and the domain boundary module from the PSIPRED () server. We used the average scores from all servers to obtain a domain boundary prediction. […]

library_books

Protein inter domain linker prediction using Random Forest and amino acid physiochemical properties

2014
BMC Bioinformatics
PMCID: 4290662
PMID: 25521329
DOI: 10.1186/1471-2105-15-S16-S8

[…] ence identity of 28.6%, and 201 linkers. DROP showed a sensitivity and precision of 41.3% and 49.4%, respectively. Varients of SVM have also been used in DomainDiscovery [], Chatterjee et al. [], and DoBo []. The above-mentioned methods, in general, have the following limitations:• Although methods that use structural information could achieve good prediction results, finding the structural inform […]

library_books

Insight from γC1 protein model for implication in cotton leaf curl disease

2013
Bioinformation
PMCID: 3705618
PMID: 23847402
DOI: 10.6026/97320630009471

[…] pathogenicity and suppression of gene silencing []. In this study, the 3D structure of CLCuDγ01-Pakistani protein has been predicted by use of the online structure prediction server, called I-TASSER. DoBo server was used to predict the domains of the protein. PROCHECK and VERIFY 3D servers were used for evaluation of the predicted γC1 structure. The final 3D model was evaluated in terms of functio […]

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DoBo institution(s)
Department of Computer Science, University of Missouri, Columbia, MO, USA

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