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Protocols

DBS-PSSM specifications

Information


Unique identifier OMICS_08388
Name DBS-PSSM
Interface Web user interface
Restrictions to use None
Input data Protein sequence in a single letter code
Computer skills Basic
Version 3.0
Stability Stable
Maintained Yes

Publication for DBS-PSSM

DBS-PSSM citations

 (4)
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

[…] d 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 were used with default parameter. The DISPLAR program was provided by Sanbo Qin and was run with default parameters. BindN […]

call_split

Novel approach for selecting the best predictor for identifying the binding sites in DNA binding proteins

2013
Nucleic Acids Res
PMCID: 3763535
PMID: 23788679
DOI: 10.1093/nar/gkt544
call_split See protocol

[…] e binding sites in DNA-binding proteins from amino acid sequence, which have either online services or available standalone programs (). The methods are BindN (), BindN+ (), BindN-RF (), DBS-Pred (), DBS-PSSM (), DNABindR (), DP-Bind with three categories, binary, BLOSUM and PSSM encoding (), metaDBSite () and NAPS (). The details about the name, features, technique, reference and link for the met […]

library_books

SVM based model generation for binding site prediction on helix turn helix motif type of transcription factors in eukaryotes

2013
Bioinformation
PMCID: 3705624
PMID: 23861565
DOI: 10.6026/97320630009500

[…] tion tool for HTH motif type of interaction studies. In view of the previous knowledge [], four web servers are available at the moment for sequence-based prediction of DNA-binding sites: DBSPRED [], DBS-PSSM [], BindN [] and DP-Bind [].Our performance measures are higher than those reported by these four studies. […]

library_books

Characterization and prediction of the binding site in DNA binding proteins: improvement of accuracy by combining residue composition, evolutionary conservation and structural parameters

2012
Nucleic Acids Res
PMCID: 3424558
PMID: 22641851
DOI: 10.1093/nar/gks405

[…] comparable to ours, though our method appears to be more sensitive. This method also outperforms the available sequence-based prediction methods of DNA-binding sites, such as DP-Bind (), DBSpred (), DBS-PSSM () and BindN () in terms of their reported accuracy, sensitivity and specificity. A very recent method, metaDBSite that integrated results from other web-servers including a few of those ment […]

Citations

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DBS-PSSM institution(s)
Department of Bioinformatics and Bioscience, Kyushu Institute of Technology, Iizuka, Fukuoka, Japan

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