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DomNet specifications

Information


Unique identifier OMICS_07075
Name DomNet
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability No
Maintained No

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Publication for DomNet

DomNet citations

 (3)
library_books

Extending Protein Domain Boundary Predictors to Detect Discontinuous Domains

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

[…] based solely on amino acid sequence composition information. pfam[–], everest[,] adda[], and fiefdom[] focus on domain boundaries prediction based on homologous alignments. chopnet[],dompro[], domnet[], pprodo[], drop[] and dobo[] use different machine learning methods to identify domain boundaries., some methods such as snapdragon[], rosettadom[] and opus-dom[] first constructed a 3d […]

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

[…] database, version 1.63 []. when tested on 48 newly added non-homologous proteins in scop version 1.65 and on casp5 targets, pprodo achieved 65.5% of prediction accuracy. ann models have also used in domnet [], dompro [], shandy [], and threadom []., ebina et al. [] developed a protein linker predictor called drop which utilizes a svm with a radial basis function (rbf) kernel. the classifier […]

library_books

A modular kernel approach for integrative analysis of protein domain boundaries

2009
BMC Genomics
PMCID: 2788374
PMID: 19958485
DOI: 10.1186/1471-2164-10-S3-S21

[…] on a curated dataset derived from the cath database. it achieved a sensitivity and specificity of 71% and 71%, respectively in the cafasp4 and was ranked among the top ab initio domain predictors. domnet [] is a recently introduced machine-learning algorithm that uses a novel compact domain profile (cd-profile). it outperformed nine other machine-learning methods on benchmark_2 dataset. domnet […]


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DomNet institution(s)
Advanced Networks Research Group, School of Information Technologies (J12), the University of Sydney, NSW, Australia; University of Sydney, NSW, Australia; Biotech Research Center, Michigan Technological University, Houghton, MI, USA; Sydney Bioinformatics Centre and the Centre for Mathematical Biology, University of Sydney, NSW, Australia
DomNet funding source(s)
Supported by the Australian Research Council under Grant DP0667266.

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