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eThread specifications

Information


Unique identifier OMICS_08131
Name eThread
Software type Package/Module
Interface Command line interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.0
Stability No
Maintained No

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Information


Unique identifier OMICS_08131
Name eThread
Interface Web user interface
Restrictions to use Academic or non-commercial use
Computer skills Basic
Version 1.0
Stability No
Maintained No

Maintainer


This tool is not available anymore.

Publication for eThread

eThread in pipeline

2013
PMCID: 3686302
PMID: 23802014
DOI: 10.3389/fgene.2013.00118

[…] under roc is a commonly used method to assess the overall performance of ranking approaches. in table , we report the area under the roc curve for individual threading methods compared to that of ethread. in the majority of cases, the performance of ethread is notably better than that of single-threading algorithms, particularly in the prediction of the chemical properties of binding […]


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eThread in publications

 (6)
PMCID: 5847522
PMID: 29560273
DOI: 10.1038/s41540-018-0050-7

[…] sites in primary and off-targets is demonstrated for a confirmed candidate for repositioning. here, we conduct pocket matching followed by vs against weakly homologous protein models constructed by ethread with binding sites predicted by efindsite. this procedure is essentially the same as that employed to reposition existing drugs to proteins linked to rare diseases. the example shown in fig. […]

PMCID: 5427563
PMID: 28499419
DOI: 10.1186/s12859-017-1675-z

[…] on 1,688 non-interacting protein pairs derived from the negatome 2.0 database []. computer models of individual proteins in negatome 2.0 were built with modeller [] using templates identified by ethread [], followed by a high-resolution structure refinement with modrefiner []., the developed pipeline to predict ppi networks is validated using e. coli as a model organism. protein interaction […]

PMCID: 4468813
PMID: 26082804
DOI: 10.1186/s13321-015-0067-5

[…] (gpcrs) and protein kinases. furthermore, we selected those proteins for which at least three weakly homologous and structurally related ligand-bound templates were detected by meta-threading using ethread []. we note that weak homology is defined by the maximum sequence identity of 40 %, and the structural similarity of ≥0.4 tm-score [] as reported by fr-tm-align []. furthermore, […]

PMCID: 4284979
PMID: 25587542
DOI: 10.1155/2014/825649

[…] for structure preparation. performance studies were conducted via the workflow-enabled science gateway mosgrid (molecular simulation grid). a. ragothaman et al. in the paper entitled “developing ethread pipeline using saga-pilot abstraction for large-scale structural bioinformatics” present a cloud infrastructure for running ethread, a metathreading protein structure modelling tool […]

PMCID: 4066679
PMID: 24995285
DOI: 10.1155/2014/348725

[…] as prokaryotes is large typically containing many thousands, prohibiting their application as a genome-wide structural systems biology tool. to leverage its utility, we have developed a pipeline for ethread—a meta-threading protein structure modeling tool, that can use computational resources efficiently and effectively. we employ a pilot-based approach that supports seamless data and task-level […]


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eThread institution(s)
Center for Computation & Technology, Louisiana State University, Baton Rouge, LA, USA

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