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Protocols

KYG specifications

Information


Unique identifier OMICS_03030
Name KYG
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Publication for KYG

KYG citations

 (3)
library_books

Non Coding RNAs in Lung Cancer: Contribution of Bioinformatics Analysis to the Development of Non Invasive Diagnostic Tools

2016
Genes
PMCID: 5295003
PMID: 28035947
DOI: 10.3390/genes8010008

[…] chine learning classifiers [,,], whereas Pprint predicts RNA binding sites using evolutionary position-specific scoring matrix (PSSM) information combined with a support vector machine (SVM) [,]. The KYG algorithm focuses on the structure and calculates binding regions by applying a position-specific multiple sequence profile on protein-RNA structures from PDB, also without biochemical or function […]

call_split

A Large Scale Assessment of Nucleic Acids Binding Site Prediction Programs

2015
PLoS Comput Biol
PMCID: 4683125
PMID: 26681179
DOI: 10.1371/journal.pcbi.1004639
call_split See protocol

[…] ameter. aaRNA was used by inputting the structure file with default parameters. RNABindR and RNABindRPlus were predicted with default parameters, while removing 95% sequence identity in RNABindRPlus. KYG was predicted with command line using “method_type = 8” option. RBscore_SVM was based on the training set of R246. DBS-PSSM, DBS-Pred, RBRIdent, PPRInt, PRBR, DNABind, RBRDetector and ProteDNA wer […]

call_split

UPF201 Archaeal Specific Family Members Reveal Structural Similarity to RNA Binding Proteins but Low Likelihood for RNA Binding Function

2008
PLoS One
PMCID: 2596488
PMID: 19079550
DOI: 10.1371/journal.pone.0003903
call_split See protocol

[…] cess.html) was used, though none was identified . 6) Putative RNA binding residues were identified using BindN (http://bioinfo.ggc.org/bindn/), RNAbindR (http://bindr.gdcb.iastate.edu/RNABindR/), and KYG (http://yayoi.kansai.jaea.go.jp/qbg/kyg/index.php) –. 7) Conserved residues were mapped onto the structure using ConSurf . 8) For phylogenetic analysis the structure based multiple sequence alignm […]

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KYG institution(s)
Quantum Bioinformatics Team, Center for Computational Science and Engineering, Japan Atomic Energy Agency, Kizu-cho, Souraku-gun, Kyoto, Japan

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