Tag: Predicting

RIP 1.1 – Predicting Target Genes of Transcription Factors

RIP 1.1

:: DESCRIPTION

RIP (regulatory interaction predictor) is a machine learning approach that inferred 73,923 RIs for 301 human TFs and 11,263 target genes with considerably good quality and 4,516 RIs with very high quality. The inference of RIs is independent of any specific condition.

::DEVELOPER

EILSLABS

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows
  • R package

:: DOWNLOAD

 RIP

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Aug 15;27(16):2239-47. doi: 10.1093/bioinformatics/btr366. Epub 2011 Jun 20.
RIP: the regulatory interaction predictor–a machine learning-based approach for predicting target genes of transcription factors.
Bauer T, Eils R, König R.

ETAscape – Cytoscape plugin for Predicting Protein Function based on Evolutionarily Important Structural Motifs

ETAscape

:: DESCRIPTION

The ETAscape Cytoscape plugin allows users to make predictions and visualize the basis for predictions of protein function based on evolutionarily important structural motifs.

::DEVELOPER

Lichtarge Computational Biology Lab

:: SCREENSHOTS

ETAscape

:: REQUIREMENTS

:: DOWNLOAD

 ETAscape

:: MORE INFORMATION

Citation:

Bioinformatics. 2012 Aug 15;28(16):2186-8. doi: 10.1093/bioinformatics/bts331. Epub 2012 Jun 11.
ETAscape: analyzing protein networks to predict enzymatic function and substrates in Cytoscape.
Bachman BJ, Venner E, Lua RC, Erdin S, Lichtarge O.

firestar – Predicting Functional Residues from Structural Templates and Alignment Reliability

firestar

:: DESCRIPTION

firestar is a server for predicting catalytic and ligand-binding residues in protein sequences.firestar makes predictions of functionally important residues using the large inventory of functionally important residues in the FireDB[3] database. The reliability of the transfer of functional information between the functionally important residues in FireDB and the query sequence is evaluated via the local residue conservation between the two sequences.

::DEVELOPER

STRUCTURAL COMPUTATIONAL BIOLOGY GROUP

:: SCREENSHOTS

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 No

:: MORE INFORMATION

Citation

firestar–advances in the prediction of functionally important residues.
Lopez G, Maietta P, Rodriguez JM, Valencia A, Tress ML.
Nucleic Acids Res. 2011 Jul;39(Web Server issue):W235-41. Epub 2011 Jun 14.