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Information


Unique identifier OMICS_03027
Name Pprint
Alternative name Prediction of Protein RNA-Interaction
Interface Web user interface
Restrictions to use None
Input data An amino acid sequence.
Input format FASTA
Output data RNA-interacting residues
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


Publication for Prediction of Protein RNA-Interaction

Pprint citations

 (5)
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

[…] ical profile Hidden Markov Model (HMM)) using propensities of individual residues from PDB [,,]. The RPISeq software calculates interactions using different machine 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 an […]

call_split

The HEX 110 Hexamerin Is a Cytoplasmic and Nucleolar Protein in the Ovaries of Apis mellifera

2016
PLoS One
PMCID: 4783013
PMID: 26954256
DOI: 10.1371/journal.pone.0151035
call_split See protocol

[…] Potential RNA-binding sites were searched in the HEX 110 sequence using RNABindR, BindN, PPRint, SVM and RNABindRPlus softwares [–]. We selected the most significant motifs, and only the alignments passing a threshold of 80% were considered as significant. The cNLS Mapper tool (http://nls […]

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

[…] le 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 and BindN+ were used by defau […]

library_books

Prediction of RNA Binding Residues: An Extensive Analysis Based on Structure and Function to Select the Best Predictor

2014
PLoS One
PMCID: 3962366
PMID: 24658593
DOI: 10.1371/journal.pone.0091140

[…] The accuracy of all the methods in both datasets lies between 55–71%. BindN+ and RNABindR v2.0 showed the best performance in both datasets at the distance cutoff of ≤3.5 Å and ≤6.0 Å, respectively. Pprint and NAPS performed well with an average accuracy of 66% and 61%, respectively. The performance of the method RNAProB is poor for the newly crystallized protein-RNA complex structures with the a […]

library_books

Predicting RNA binding residues from evolutionary information and sequence conservation

2010
BMC Genomics
PMCID: 3005934
PMID: 21143803
DOI: 10.1186/1471-2164-11-S4-S2

[…] er relative to the estimates obtained using sequence-based cross-validation. RNAProB, BindN, RISP, PRINTR and PiRaNhA are predictors that report performance window-based k-fold cross-validation while Pprint and RNABindR report performance with sequence-based k-fold cross-validation. The predictors evaluated with window-based k-fold cross-validation have superior performance than those with sequenc […]

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Pprint institution(s)
Bioinformatics Centre, Institute of Microbial Technology, Chandigarh, India

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