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JET specifications

Information


Unique identifier OMICS_13056
Name JET
Alternative name Joint Evolutionary Trees
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format MUSCLE format
Output data Set of interesting clusters
Output format VMD format
Operating system Unix/Linux, Mac OS
Programming languages Java
Computer skills Advanced
Stability Stable
Requirements
ClustalW, Naccess, BLAST Toolkit
Maintained Yes

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Versioning


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Documentation


Maintainer


  • person_outline Alessandra Carbone

Publication for Joint Evolutionary Trees

JET citations

 (3)
library_books

Meet U: Educating through research immersion

2018
PLoS Comput Biol
PMCID: 5854232
PMID: 29543809
DOI: 10.1371/journal.pcbi.1005992

[…] diversity of implemented strategies (). For example, one team implemented a Fast Fourier Transform (FFT)-based engine for the sampling step and a scoring function including predictions from the tool Joint Evolutionary Trees2 (JET2) [], which uses residue conservation, physicochemical, and geometrical properties of protein interfaces (, left panel). They obtained very good results on the ribonucle […]

library_books

Local Geometry and Evolutionary Conservation of Protein Surfaces Reveal the Multiple Recognition Patches in Protein Protein Interactions

2015
PLoS Comput Biol
PMCID: 4686965
PMID: 26690684
DOI: 10.1371/journal.pcbi.1004580

[…] these machine learning approaches sometimes perform very well, they generally do not provide a clear understanding of the molecular determinants of protein-protein association.We previously developed Joint Evolutionary Trees (JET) for protein interface prediction []. JET relies on the assumption that protein interfaces are composed of a core, formed by highly conserved residues having particular p […]

library_books

Recent advances in functional region prediction by using structural and evolutionary information – Remaining problems and future extensions

2013
Comput Struct Biotechnol J
PMCID: 3962155
PMID: 24688747
DOI: 10.5936/csbj.201308007

[…] o improve the prediction accuracy. Engelen et al. [] addressed this problem by integrating the conservation information and the specific physicochemical properties of the residues. They developed the Joint Evolutionary Trees (JET) method [], to detect protein interfaces, the core residues involved in the folding process, and the residues susceptible to site-directed mutagenesis and relevant to mol […]

Citations

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JET institution(s)
Génomique Analytique, Université Pierre et Marie Curie-Paris, UMR S511, Paris, France; INSERM, UMR 511, Paris, France; Laboratoire de Biochimie Théorique, IBPC, Paris, France; Institut de Biologie et Chimie des Protéines, CNRS UMR 5086, Université de Lyon, Lyon, France
JET funding source(s)
Carried out with the financial support of the AFM/IBM/CNRS Decrypthon project and of INSERM.

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