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Protocols

LOGICOIL specifications

Information


Unique identifier OMICS_07852
Name LOGICOIL
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Thomas L. Vincent

Information


Unique identifier OMICS_07852
Name LOGICOIL
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Thomas L. Vincent

Publication for LOGICOIL

LOGICOIL citations

 (8)
library_books

A new class of hybrid secretion system is employed in Pseudomonas amyloid biogenesis

2017
Nat Commun
PMCID: 5557850
PMID: 28811582
DOI: 10.1038/s41467-017-00361-6

[…] The full-length protein was modelled by generating an idealised trimeric coiled-coil. This was done using the converged results from coiled-coil prediction software; COILS/PCOILS and LOGICOIL followed by CC Builder V1.0 . The coiled-coil was placed at a distance from FapFβ to result in a partially extended linker conformation and Modeller was used to generate the initial conformat […]

library_books

RNF41 interacts with the VPS52 subunit of the GARP and EARP complexes

2017
PLoS One
PMCID: 5439944
PMID: 28542518
DOI: 10.1371/journal.pone.0178132

[…] ncated forms were co-expressed with VPS52 in HEK293T cells, confirmed the MAPPIT results. Of note, the L163Q mutant showed no difference in stability compared to WT RNF41 (data not shown).The program Logicoil [], predicted the CC regions of RNF41 to form a trimer, which corresponds to the observations in a recently published paper based on chemical crosslinking and size exclusion chromatography [] […]

call_split

Electron Microscopy Structural Insights into CPAP Oligomeric Behavior: A Plausible Assembly Process of a Supramolecular Scaffold of the Centrosome

2017
Front Mol Biosci
PMCID: 5366329
PMID: 28396859
DOI: 10.3389/fmolb.2017.00017
call_split See protocol

[…] ture was predicted with Jpred4 (Drozdetskiy et al., ); for the prediction of CC regions the web server COILS (Lupas et al., ) was used and, finally, the web servers PrOCoils (Mahrenholz et al., ) and LOGICOIL (Vincent et al., ) were employed to predict the oligomeric state probability of the CC sequence. The atomic modeling of CC4/CC5, CCGb-linker, and G-box regions of HsCPAP, was carried out with […]

library_books

ACCORD: an assessment tool to determine the orientation of homodimeric coiled coils

2017
Sci Rep
PMCID: 5339707
PMID: 28266564
DOI: 10.1038/srep43318

[…] ce of a different oligomeric state was detected, but the major peak always corresponded to a dimer of parallel CCDs (). This is an extremely good result compared to those of other prediction methods. LOGICOIL is very powerful for analysing the oligomeric state and orientation of CCDs; however, its prediction of the orientation of dimeric CCs was not sufficiently accurate (). The first predictions […]

library_books

Self sorting heterodimeric coiled coil peptides with defined and tuneable self assembly properties

2015
Sci Rep
PMCID: 4570195
PMID: 26370878
DOI: 10.1038/srep14063

[…] measured for all ratios (). This confirmed that all four peptide combinations primarily associate in a 1:1 ratio. Formation of dimers was verified using several predictive analysing tools, including Logicoil, RFCoil, and PrOCoil.Formation of transient or less stable oligomers can however not be fully excluded but MD simulations further supported formation of stable parallel heterodimers for all p […]

library_books

Analysis of AKAP7γ Dimerization

2015
PMCID: 4568377
PMID: 26417456
DOI: 10.1155/2015/371626

[…] le mechanisms include posttranslational modification driven interactions and coiled-coil interactions [–]. Analysis of the AKAP7γ sequence using the PredictProtein website as well as both MARCOIL and LOGICOIL web resources supports these possibilities for AKAP7γ. Testing these potential mechanisms for oligomerization will help in delineating the means of AKAP7γ complex formation.Signaling proteins […]

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LOGICOIL institution(s)
School of Chemistry, University of Bristol, Bristol, UK

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