CCMpred specifications

Information


Unique identifier OMICS_05287
Name CCMpred
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C
Parallelization CUDA
License GNU Affero General Public License version 3
Computer skills Advanced
Stability Stable
Maintained Yes

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Documentation


Maintainer


  • person_outline Johannes Söding <>

Publication for CCMpred

CCMpred in publications

 (10)
PMCID: 5713875
PMID: 29199978
DOI: 10.1107/S2059798317016436

[…] employing a cooperative statistical model. examples of implementations that employ a pseudo-likelihood maximization model can be found in applications such as gremlin (ovchinnikov et al., 2014) and ccmpred (seemayer et al., 2014). other implementations include sparse covariance matrix-inversion models such as psicov (seemayer et al., 2014; jones et al., 2012) or mean-field direct coupling […]

PMCID: 5836854
PMID: 28901583
DOI: 10.1002/prot.25379

[…] method to derive covariation‐based contacts (jones et al. ). at its core metapsicov is a meta‐predictor based on different covariation prediction algorithms, including mfdca (kaján et al. ), ccmpred (seemayer et al. ) and psicov (jones et al. ). when there isn't sufficient sequence data available to allow effective covariation analysis, the neural network is able to exploit information […]

PMCID: 5428263
PMID: 28303031
DOI: 10.1038/s41598-017-00320-7

[…] with the default parameters. the final secondary structure used for further analyses was determined using a majority voting approach on the output of each algorithm., six ec algorithms (metapsicov, ccmpred, pconsc2, plmdca, epc-map and raptorx) were selected to predict all possible e1e2 residue couples’ propensity of interaction, –. when possible, the algorithm was fed with the refined e1e2 […]

PMCID: 5114557
PMID: 27857150
DOI: 10.1038/srep36679

[…] to the randomly determined uniprot distribution in nostruct (see methods for details). shows a comparison between the homologs distribution in nostruct and noumenon., we then tested the psicov and ccmpred unsupervised contact prediction methods on the noumenon dataset and compared the results to the ones obtained on the widely adopted psicov dataset. we selected psicov because it is a landmark […]

PMCID: 5860252
PMID: 28171606
DOI: 10.1093/bioinformatics/btw618

[…] couplings as parameters of a probabilistic graphical model (markov random field) by maximizing its pseudo-likelihood. this approach has several implementations, including plmdca (), gremlin () and ccmpred (). gremlin has been tested on 329 protein targets selected from the continuous, automated model evaluation (cameo) () and shown to outperform psicov, plmdca and mfdca. another tool, epc-map […]


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CCMpred institution(s)
Gene Center, LMU Munich, Munich; Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
CCMpred funding source(s)
This work was funded by the Deutsche Forschungsgemeinschaft (Grants GRK1721 and SFB646) and the Bavarian Center for Molecular Biosystems (BioSysNet).

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