Paircoil protocols

View Paircoil computational protocol

Paircoil statistics

To access cutting-edge analytics on consensus tools, life science contexts and associated fields, you will need to subscribe to our premium service.

Subscribe
info

Citations per year

Citations chart
info

Popular tool citations

chevron_left Coiled-coil domain prediction chevron_right
Popular tools chart
info

Tool usage distribution map

Tool usage distribution map
info

Associated diseases

Associated diseases

Paircoil specifications

Information


Unique identifier OMICS_07845
Name Paircoil
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
Computer skills Advanced
Version 2.0
Stability Stable
Maintained Yes

Versioning


Add your version

Maintainer


  • person_outline Paircoil <>

Information


Unique identifier OMICS_07845
Name Paircoil
Interface Web user interface
Restrictions to use None
Computer skills Basic
Version 2.0
Stability Stable
Maintained Yes

Maintainer


  • person_outline Paircoil <>

Publications for Paircoil

Paircoil in pipelines

 (2)
2017
PMCID: 5291535
PMID: 28158222
DOI: 10.1371/journal.pone.0171181

[…] nbs–lrr proteins from two wild peanut were extracted using hmmer [] and in-house perl script. tir, nbs, and lrr domains were confirmed in the pfam database. the cc domain was surveyed using paircoil2 (http://groups.csail.mit.edu/cb/paircoil2/). the p-score cutoff was 0.03., multiple sequence alignment of cnl and tnl full-length proteins from a. duranensis and a. ipaënsis was performed […]

2011
PMCID: 3107778
PMID: 21554724
DOI: 10.1186/1471-2180-11-95

[…] (encompassing residues 4-43 and 49-79, respectively). both helical segments are amphipathic but only the c-terminal one is predicted to form a coiled-coil structure http://groups.csail.mit.edu/cb/paircoil/paircoil.html. yqic secondary structure was experimentally determined by its far uv circular dichroism spectrum (figure ), which showed a typical signature of an alpha helical protein. […]


To access a full list of citations, you will need to upgrade to our premium service.

Paircoil in publications

 (69)
PMCID: 5777259
PMID: 29191834
DOI: 10.1074/jbc.M117.806521

[…] and 6a contain 5 and 4 charge changes compared with tpm1.8 and tpm1.12, respectively. exon 9d contains 3 charge changes compared with tpm1.8 and 11 charge changes compared with tpm1.12. the program paircoil2 () predicts that only the c-terminal ends of tpm1.8 and tpm1.12 are affected by differences in their amino acid sequence. in the case of tpm3.1, paircoil2 indicates a slightly reduced […]

PMCID: 5614648
PMID: 28910277
DOI: 10.1371/journal.pgen.1006986

[…] thereby deleting the ~600 base pairs. worms from plates containing rollers and dumpys were screened by pcr and homozygous mutants were isolated., protein domains were determined using psipred [] and paircoil2 []. protein sequences were analyzed using clustal omega []. proline-rich regions of proteins have been shown to bind microtubules []. the proline content of amino acids 1–149 is 14% […]

PMCID: 5633384
PMID: 28839119
DOI: 10.1534/g3.117.300193

[…] bank. for each protein, we calculate the fraction of residues which are ordered and established a statistical difference using a kolmogorov–smirnov test. coiled-coil regions were predicted using paircoil2 ()., we took dn/ds values for s. cerevisiae genes from , and functional annotations from . we examined the distribution of dn/ds for each functional class and tested for significant […]

PMCID: 5291535
PMID: 28158222
DOI: 10.1371/journal.pone.0171181

[…] nbs–lrr proteins from two wild peanut were extracted using hmmer [] and in-house perl script. tir, nbs, and lrr domains were confirmed in the pfam database. the cc domain was surveyed using paircoil2 (http://groups.csail.mit.edu/cb/paircoil2/). the p-score cutoff was 0.03., multiple sequence alignment of cnl and tnl full-length proteins from a. duranensis and a. ipaënsis was performed […]

PMCID: 5114598
PMID: 27834372
DOI: 10.1038/ncomms13390

[…] cutoff). genes that contained pf00931 (nb-arc) domain were considered to be r genes. the lrr and tir domains were also assigned based on hmmsearch results. the cc domain was discovered using paircoil2 (ref. ). resistance gene clusters were determined by their physical position order. the parameter to define a cluster was two or more r genes that occurred within a maximum of ten non-r […]


To access a full list of publications, you will need to upgrade to our premium service.

Paircoil institution(s)
Mathematics Department, Computer Science and Artificial Intelligence LaboratoryCambridge, MA, USA

Paircoil reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review Paircoil