CCBuilder protocols

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CCBuilder specifications

Information


Unique identifier OMICS_05289
Name CCBuilder
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Derek N. Woolfson <>

Publications for CCBuilder

CCBuilder in pipeline

2018
PMCID: 5944148
PMID: 29743008
DOI: 10.1186/s12858-018-0093-9

[…] were measured using a high impedance electrometer (keithley 617), and analyzed using the goldman-hodgkin-katz equation []., initial models of hexamer and octamer channels were constructed using the ccbuilder tool [] without prior structural information. both channels were simulated in a pope bilayer containing a 1 m kcl solution (hexamer system about 66.000 atoms, octamer system about 90.000 […]


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CCBuilder in publications

 (7)
PMCID: 5944148
PMID: 29743008
DOI: 10.1186/s12858-018-0093-9

[…] were measured using a high impedance electrometer (keithley 617), and analyzed using the goldman-hodgkin-katz equation []., initial models of hexamer and octamer channels were constructed using the ccbuilder tool [] without prior structural information. both channels were simulated in a pope bilayer containing a 1 m kcl solution (hexamer system about 66.000 atoms, octamer system about 90.000 […]

PMCID: 5829827
PMID: 29487240
DOI: 10.1128/mBio.02052-17

[…] full-length bvgsδ65 cys variants (called bvgsδ65fl) were used to determine the effect of cys substitution on bvgs activity., models of the coiled coils were prepared in registers k and p using ccbuilder (). the models were processed for molecular dynamics (md) simulations using the gromacs suite of programs, version 5.0.4, and the gromos 43a2 force field (). c-terminal and n-terminal helix […]

PMCID: 5851934
PMID: 29552648
DOI: 10.1016/j.synbio.2017.11.002

[…] protein backbone perturbations and amino acid sequence mutations to design proteins with desired catalytic activity. in addition, a number of computational tools (e.g. dezymer , , orbit , rosetta , ccbuilder , , and protein wisdom ) are aimed at de novo enzyme design by exploiting the underlying protein biochemistry and biophysics. however certain enzyme properties such as configurational […]

PMCID: 5025789
PMID: 27586688
DOI: 10.1038/ncomms12629

[…] the following modelled regions: 110–192 (cc1, 82 aa), 250–256 (7 aa), 345–364 (20 aa) and 365–391 (27 aa). the long wt cc1 (110–192) and the short mutant cc1 (110–133) fragments were generated using ccbuilder with a radius of 5.07 å, a superhelical pitch of 225.8 å and an interface angle of 26.42°. the fragment building corresponding to the disordered region between cc2-lz and zf domains […]

PMCID: 4810494
PMID: 26933056
DOI: 10.1128/mBio.02089-15

[…] leu residues of the motif were replaced by ala residues to loosen its hydrophobic interface (). in silico, we generated 10 models for each of the 6 sequences of the arg699–ala719 segment with the ccbuilder program and determined for each variant the value of the energy of interaction per residue using the coilcheck+ program (). as anticipated, the progressive introduction of leu residues led […]


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CCBuilder institution(s)
School of Chemistry, University of Bristol, Cantock’s Close, Bristol, UK; School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk, Bristol, UK; BrisSynBio, University of Bristol, Life Sciences Building, Bristol, UK
CCBuilder funding source(s)
Supported by grants from the European Research Council (340764) and BBSRC/ERASynBio (BB/M005615/1).

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