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PPRODO specifications

Information


Unique identifier OMICS_07074
Name PPRODO
Alternative name Prediction of PROtein DOmain boundaries
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 Prediction of PROtein DOmain boundaries

PPRODO citations

 (4)
library_books

Extending Protein Domain Boundary Predictors to Detect Discontinuous Domains

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

[…] ed 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 model and then ex […]

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

[…] proteins was obtained from the structural classification of proteins (SCOP) 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 utili […]

library_books

Ab initio and homology based prediction of protein domains by recursive neural networks

2009
BMC Bioinformatics
PMCID: 2711945
PMID: 19558651
DOI: 10.1186/1471-2105-10-195

[…] on boundaries with a simple amino acid propensity index. Again boundaries were considered correct for ± 20 residues.Finally, we directly compare Ab initio and SCOP25 with the predictor in [] and with PPRODO [] and report the results in Table . In this case the two predictors are optimised for two-domain proteins rather than for a mixture of single and multiple-domain ones. For this reason we test […]

library_books

Protein Domain Boundary Predictions: A Structural Biology Perspective

2009
PMCID: 2669640
PMID: 19401756
DOI: 10.2174/1874091X00903010001

[…] on [, ] can timely provide very useful information and insights for both basic research and drug design and hence are widely welcome by science community.Several computational approaches aimed to the prediction of protein domain boundaries have been published during the last few years [, ]. Besides their intrinsic interest in genome analysis and evolution studies, they are tools that structural bi […]

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PPRODO institution(s)
School of Computational Sciences, Korea Institute for Advanced Study, Seoul, Korea

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