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NNcon specifications

Information


Unique identifier OMICS_07130
Name NNcon
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Version 1.0
Stability Stable
Maintained Yes

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Publication for NNcon

NNcon in publications

 (6)
PMCID: 5576353
PMID: 28851269
DOI: 10.1186/s12859-017-1807-5

[…] local contacts and short-range contacts, medium-range contacts are very important for reconstruction.fig. 8 , realizing the importance of contact definition at higher distance thresholds, tools like nncon [] predict contacts at both distance thresholds – 8 å and 12 å. there are, however, challenges in predicting contacts at higher distance thresholds and utilizing them to build models. the first […]

PMCID: 5398280
PMID: 28439455
DOI: 10.7717/peerj.3139

[…] and can help deal with indirect-coupling effects as well., neural networks () and deep learning (), as mentioned above, have also been used in contact map prediction. for example, the program nncon  uses a recursive 2-d neural network in which the inputs comprise an l-byl grid representing the amino acids of a protein, and the outputs are the probabilities of each pair of amino acids […]

PMCID: 4725912
PMID: 26763289
DOI: 10.1038/srep19301

[…] this feature;the difference of solvent accessibility between that predicted from sequence by sspro and the values from the model as parsed by dssp. this is similar to the secondary structure feature;nncon was used to predict the residue-residue contact probabilities based on amino acid sequence. this produced a probability for each pair of residues in the protein which indicated the likelihood […]

PMCID: 4332441
PMID: 25564011
DOI: 10.1186/s13062-014-0031-8

[…] accuracies over the 7 datasets for both the l/2 and l top-ranked predictions (average accuracy = 0.35, 0.27, respectively) (additional file : table s4). comparing cnpr to the second best method nncon, average accuracies over the 7 datasets for the l/2 and l top-ranked predictions increased by 0.061 (17.6%) and 0.031 (11.5%), respectively (table , additional file : table s4). thirdly, […]

PMCID: 3247924
PMID: 22082126
DOI: 10.1186/1471-2105-12-444

[…] predictor could be boosted by combining the correlated mutation search with such approaches. this could include for example specialized beta-sheet contact prediction algorithms such as applied by nncon []., the dependence of rmrcm performance on the number of sequences in the input alignment as observed with the casp datasets, was similar to what was observed for the artificial datasets (see […]


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NNcon institution(s)
Computer Science Department, Informatics Institute, University of Missouri, Columbia, MO, USA

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