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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

 (14)
library_books

Structure of the calcium dependent type 2 secretion pseudopilus

2017
PMCID: 5705324
PMID: 28993624
DOI: 10.1038/s41564-017-0041-2

[…] of pulg sequence was obtained with the consurf server (300 homologous sequences asked with between 35 and 95% identity). co-evolutionary contact predictions for pulg were obtained with the gremlin tool. the ratio between the number of sequences used by gremlin and the length of the query was 14.9. helical propensity of pulg residues f1-r56 was computed with the psipred and jpred4 […]

library_books

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

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

[…] from tm predictions (polyphobius, memsat-svm) and secondary structure predictions (psipred server). modeling was facilitated by distance constraints of evolutionarily coupled amino acid pairs (gremlin) () ; these pairs are predicted to have co-evolved based on the analysis of a large dataset of aligned hrd1 sequences from different species. for the co-evolution analysis by gremlin, […]

library_books

Inferring repeat protein energetics from evolutionary information

2017
PMCID: 5491312
PMID: 28617812
DOI: 10.1371/journal.pcbi.1005584

[…] simplifying the energetic description of complex natural systems []., in the last years new methods to analyze correlated mutations across a family of proteins have arisen (mfdca [], plmdca [, ], gremlin [] to name a few). the main hypothesis behind these methods is that biochemical changes produced by a point mutation should be compensated by other mutations (along evolutionary timescales) […]

library_books

Exploring RNA conformational space under sparse distance restraints

2017
PMCID: 5345030
PMID: 28281575
DOI: 10.1038/srep44074

[…] sets., for each molecule, the restraints data-sets included: the observed base pairs defined by the moderna server, the base pairs predicted by the rnafold program and contacts predicted by the gremlin method. while the former two methods provide a fixed set of base pairs, the contacts predicted by the latter method, which may or may not be base paired, constitutes a set of a few hundred […]

library_books

Structure based Markov random field model for representing evolutionary constraints on functional sites

2016
PMCID: 4765150
PMID: 26911566
DOI: 10.1186/s12859-016-0948-2

[…] more accurately represent functional constraints. to assess the effectiveness of the protein structure-based mrf architecture, we compared the smrf approach with the state-of-the-art mrf methods gremlin [] and psicov [] using the recommended default options. additionally, we built a random predictor by randomly permutating the coevolution scores of the smrf 100 times and calculating […]

library_books

Coevolution Analysis of HIV 1 Envelope Glycoprotein Complex

2015
PMCID: 4651434
PMID: 26579711
DOI: 10.1371/journal.pone.0143245

[…] and indirect correlations that arise from phylogenetic relationships within the sequences. recent methodological improvements, incorporated in methods such as psicov [], dca [, ], plmdca [] or gremlin [, ] have overcome the drawbacks and demonstrated enormous accuracy in predicting real couplings and coevolution., the majority of previous work, that studied coevolution within hiv-1 env […]


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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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