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Protocols

GREMLIN specifications

Information


Unique identifier OMICS_13940
Name GREMLIN
Alternative names Generative REgularized ModeLs of proteINs, OPENSEQ
Interface Web user interface
Restrictions to use None
Input data An amino acid sequence or protein
Input format FASTA
Programming languages MATLAB, Perl
Computer skills Basic
Version 2.01
Stability Stable
Maintained Yes

Documentation


Information


Unique identifier OMICS_13940
Name GREMLIN
Alternative names Generative REgularized ModeLs of proteINs, OPENSEQ
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages MATLAB, Perl
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Documentation


Publications for Generative REgularized ModeLs of proteINs

GREMLIN citations

 (34)
library_books

CoeViz: A Web Based Integrative Platform for Interactive Visualization of Large Similarity and Distance Matrices

2018
PMCID: 5798608
PMID: 29423399
DOI: 10.3390/data3010004

[…] servers for coevolution analysis in proteins were evaluated. Based on the original publications, where some visualization means for the results were presented, we tried ConEVA [], EVcouplings [], and GREMLIN [] using the same human ESR1 protein.The ConEVA web-server was not responsive after multiple attempts, so it may be no longer supported. EVcouplings accepted the protein input with the remaini […]

library_books

Dynamics of Intact MexAB OprM Efflux Pump: Focusing on the MexA OprM Interface

2017
Sci Rep
PMCID: 5705723
PMID: 29184094
DOI: 10.1038/s41598-017-16497-w

[…] prM interface and in particular the interacting residue pairs between them, we performed a sequence covariation analysis for these two proteins. Two online tools for performing this type of analysis, GREMLIN and EVComplex, were used to identify residue pairs that show covariation with family members of MexA and OprM. Application of both methods to bacterial protein complexes with experimentally-so […]

library_books

Approaches to ab initio molecular replacement of α helical transmembrane proteins

2017
Acta Crystallogr D Struct Biol
PMCID: 5713875
PMID: 29199978
DOI: 10.1107/S2059798317016436

[…] Solution was then attempted with models generated by the GREMLIN modelling protocol. The results are displayed in Fig. 1, with a graphical summary shown in Supplementary Fig. S6 and an analysis of the TM scores shown in Supplementary Fig. S7. GREMLIN was ab […]

library_books

Modeling protein quaternary structure of homo and hetero oligomers beyond binary interactions by homology

2017
Sci Rep
PMCID: 5585393
PMID: 28874689
DOI: 10.1038/s41598-017-09654-8

[…] he SVM-predicted QS-score is compared to other ranking criteria: (i) a physics-based docking score as described in ref. , (ii) a co-evolution based score representing the agreement between models and GREMLIN predicted contacts (see “Co-evolution Agreement” in Material and Methods), (iii) a sequence identity criteria that would always rank first the model whose template has the highest sequence ide […]

library_books

Role of water and protein dynamics in proton pumping by respiratory complex I

2017
Sci Rep
PMCID: 5552823
PMID: 28798393
DOI: 10.1038/s41598-017-07930-1

[…] two enzymes classes (e.g. Thermus and Bovine), but the functional role is shared. This viewpoint is also supported by the coevolution analysis performed on Nqo4/6 sequences using two different tools, GREMLIN and EVcomplex. The data from GREMLIN (normalized coupling strength >1) and EVcomplex (EVcomplex score ~0.53) suggests that Thr64 in Nqo4 and Arg83 in Nqo6 are evolutionarily coupled such that […]

library_books

Cryo EM structure of the protein conducting ERAD channel Hrd1 in complex with Hrd3

2017
Nature
PMCID: 5736104
PMID: 28682307
DOI: 10.1038/nature23314

[…] codes EMD-8639 and EMD-8638, respectively. The raw cryo-EM data were deposited to EMPIAR (accession code EMPIAR-10099). An interactive session of models with co-evolution data can be found at http://gremlin.bakerlab.org/hrd. […]

Citations

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GREMLIN institution(s)
Department of Biochemistry, Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA; Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA; Facebook Inc, Seattle, WA, USA
GREMLIN funding source(s)
Supported by the National Institutes of Health (grant 1R01GM092802-04), the National Institute of General Medical Studies (grant P41 GM103533) and by the Defense Threat Reduction Agency (grant N00024-10-D-6318/0024-02).

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