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DeepCNF specifications

Information


Unique identifier OMICS_17373
Name DeepCNF
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Version 1.00
Stability Stable
Source code URL https://ttic.uchicago.edu/~wangsheng/DeepCNF_D_package_v1.00.tar.gz
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Sheng Wang

Publication for DeepCNF

DeepCNF citations

 (6)
library_books

Polymorphism in merozoite surface protein 7E of Plasmodium vivax in Thailand: Natural selection related to protein secondary structure

2018
PLoS One
PMCID: 5931635
PMID: 29718980
DOI: 10.1371/journal.pone.0196765

[…] epeats Finder version 4.0 program []. Protein secondary structure prediction was determined by Deep Convolutional Neural Filed program (DeepCNF) implemented in the RaptorX-Property Web-Server []. The DeepCNF method has been validated to outperform other methods that achieved >70% accuracy in eight-state protein structure prediction []. Protein disordered or intrinsically unstructured regions were […]

library_books

Opportunities and obstacles for deep learning in biology and medicine

2018
PMCID: 5938574
PMID: 29618526
DOI: 10.1098/rsif.2017.0387

[…] networks. In 2014, Zhou & Troyanskaya [] demonstrated that they could improve Q8 accuracy by using a deep supervised and convolutional generative stochastic network. In 2016, Wang et al. developed a DeepCNF model that improved Q3 and Q8 accuracy as well as prediction of solvent accessibility and disorder regions [,]. DeepCNF achieved a higher Q3 accuracy than the standard maintained by PSIPRED fo […]

library_books

DeepSF: deep convolutional neural network for mapping protein sequences to folds

2017
Bioinformatics
PMCID: 5905591
PMID: 29228193
DOI: 10.1093/bioinformatics/btx780

[…] secondary structure, we analyzed how the different quality of predicted secondary structure influences the fold prediction. We generated predicted secondary structure using four methods: SCRATCH (), DeepCNF (), DNSS () and PSIPRED (), which were used for fold classification on the CASP dataset, respectively. The results are shown in . For top 1 fold prediction, higher secondary structure predicti […]

library_books

C terminal lysine repeats in Streptomyces topoisomerase I stabilize the enzyme–DNA complex and confer high enzyme processivity

2017
Nucleic Acids Res
PMCID: 5714199
PMID: 28981718
DOI: 10.1093/nar/gkx827

[…] is consistent with the higher incidence of β-structures in the E. coli TopA CTD (32%, based on crystallographic data) compared to the S. coelicolor TopA CTD (16%, based on structure prediction using DeepCNF (Deep Convolutional Neural Fields) ()). The recent sequence and structure analysis of M. tuberculosis TopA revealed that its CTD encompasses four repeated subdomains and ends with a lysine-ric […]

library_books

Sixty five years of the long march in protein secondary structure prediction: the final stretch?

2016
Brief Bioinform
PMCID: 5952956
PMID: 28040746
DOI: 10.1093/bib/bbw129

[…] twork (SPINE) [] in 2007, 82% by Structural Property prediction with Integrated DEep neuRal network 2 (SPIDER2) [] in 2015, to 84% for several test data sets by Deep Convolution Neural Field network (DeepCNF) [] in 2016. Although accuracies reported by different methods are not always directly comparable because of different data sets being used, there is a clear trend of a slow but steady improve […]

library_books

Protein Secondary Structure Prediction Using Deep Convolutional Neural Fields

2016
Sci Rep
PMCID: 4707437
PMID: 26752681
DOI: 10.1038/srep18962

[…] We have presented a new sequence labeling method, called DeepCNF (Deep Convolutional Neural Fields), for protein secondary structure prediction. This new method can not only model complex sequence-structure relationship by a deep hierarchical architecture, […]

Citations

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DeepCNF institution(s)
Department of Human Genetics, University of Chicago, Chicago, IL, USA; Toyota Technological Institute at Chicago, Chicago, IL, USA; MoE Key Laboratory of Developmental Genetics and Neuropsychiatric Diseases, Bio-X Center, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China

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