FUGUE protocols

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FUGUE specifications

Information


Unique identifier OMICS_06086
Name FUGUE
Software type Package/Module
Interface Command line interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux
Programming languages C
Computer skills Advanced
Stability Stable
Maintained Yes

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  • person_outline FUGUE <>

Information


Unique identifier OMICS_06086
Name FUGUE
Interface Web user interface
Restrictions to use Academic or non-commercial use
Programming languages C
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline FUGUE <>

Publication for FUGUE

FUGUE in pipelines

 (3)
2014
PMCID: 4096751
PMID: 24997568
DOI: 10.1186/1756-0500-7-435

[…] [], hhrep (http://toolkit.tuebingen.mpg.de/hhrep) [] and repro (http://www.ibi.vu.nl/programs/reprowww/) []. fold recognition was performed using fugue (http://tardis.nibio.go.jp/fugue/) and hhpred (http://toolkit.tuebingen.mpg.de/hhpred/, with the hmm database of pdb70_18dec10) [] using the three segments defined in figure  as queries., interaction sites on big3 and phb2 […]

2008
PMCID: 2459191
PMID: 18590572
DOI: 10.1186/1471-2105-9-298

[…] in addition to sequence information. hidden markov model (hmm) method [], psi-blast [], ffas [], picasso [], and compass [] can be classified into the first method. genthreader [], 3d-pssm [], fugue [], and prospect [,] represent the second approach. currently most remote homolog detection methods are based on profile-profile alignment (ppa). some examples are sp3 method [], profnet [], […]

2007
PMCID: 1829167
PMID: 17338813
DOI: 10.1186/1471-2105-8-73

[…] -2.53, mgenthreader: 0.476, consensus servers pcons2: 0.719 and pcons5: 0,829). other highly scored templates belonged to cog1385 (1vhk/1vxz/1vhy) inbgu: 36.02 sam-t02: 0.015, sparks: -2.52, fugue: 3.92., we used the newly identified spout families as queries to carry out additional profile-hmm searches, but no new families could be identified to show similarity to the expanded spout […]


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FUGUE in publications

 (86)
PMCID: 5266723
PMID: 28184216
DOI: 10.3389/fmicb.2017.00048

[…] acetate salt (gpk-na) as previously published (toh et al., )., modeling of the p. gingivalis k4 domain based on the known structure of the cleaved adhesin domain k3 (pdb: 3m1h) was performed using fugue (shi et al., ) to generate a structural alignment, followed by orchestrar (tripos international) to build a molecular model based on that alignment. model quality was tested using the align_all […]

PMCID: 5187918
PMID: 27999256
DOI: 10.3390/ijms17122118

[…] information, such as secondary structure, solvent accessibility, and residue depth. ffas-3d remarkably outperforms ffas. moreover, shi et al. [] developed a protein fold recognition method called fugue, which can search sequences against protein fold libraries by using environment-specific substitution tables and structure-dependent gap penalties. raptor is a novel method that uses […]

PMCID: 5140013
PMID: 27980384
DOI: 10.4137/EBO.S40912

[…] environment-specific substitution tables or pseudo-energy-based functions to calculate if it is possible that a template is a fold of a target sequence., sequence-structure homology methods (like fugue and 3dpssm) fail when two proteins are structurally similar, but share little in the way of sequence homology., threading methods (such as threader) depend on data derived from solved […]

PMCID: 5063617
PMID: 27582384
DOI: 10.1091/mbc.E16-05-0332

[…] l5kc08 [pteropus alecto], and l8y7j9 [tupaia chinensis]) using clustalw (). alignment of the effectors with the jrab c-terminal fragments (corresponding to aa 880–1009 in mouse) was generated using fugue (), based on the structural alignment of the three effector proteins and their amino acid sequence information and on the sequence alignment of jrab/mical-l2 from the seven species. […]

PMCID: 5054609
PMID: 27717396
DOI: 10.1186/s13023-016-0514-z

[…] modeller []. the template was the crystal structure of the human α5β1 ectodomain (protein data bank code 3iv4) []. we aligned residues 34-612 of integrin α3 to residues 42-642 of integrin α5 with fugue [] and borrowed the structure of integrin β1 residues 26-465 from 3iv4 []. fugue utilizes environment-specific substitution tables and structure-dependent gap penalties, so that scores […]


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FUGUE institution(s)
Department of Biochemistry University of Cambridge, Cambridge, UK

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