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

:: REQUIREMENTS

Windows / Linux / Mac OsX
Java
Cytoscape

:: 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.

FSWeight 2.2 – Protein Function Prediction

FSWeight 2.2

:: DESCRIPTION

FSWeight(Functional similarity weighting) is a software for inferring the function of proteins based on its indirect interaction partners. Its sensitivity and precision are superior to Neighbour Counting, Chi2, PRODISTIN, Functional Flow, and Markov Random Field approaches. It can also be used for ranking the reliability of individual protein interactions.

::DEVELOPER

Limsoon Wong Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / Linux / MacOsX
C++ Compiler

:: DOWNLOAD

FSWeight

:: MORE INFORMATION

Citation:

Genome Inform. 2006;17(2):284-97.
Increasing confidence of protein-protein interactomes.
Chen J, Chua HN, Hsu W, Lee ML, Ng SK, Saito R, Sung WK, Wong L.

SNAP – Predicts Effect of Mutations on Protein Function

SNAP

:: DESCRIPTION

SNAP (screening for non-acceptable polymorphisms) is a method for evaluating effects of single amino acid substitutions on protein function.SNAP identifies over 80% of the non-neutral mutations at 77% accuracy and over 76% of the neutral mutations at 80% accuracy at its default threshold. Each prediction is associated with a reliability index that correlates with accuracy and thereby enables experimentalists to zoom into the most promising predictions.

::DEVELOPER

Yana Bromberg in Rost Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

available upon request.

:: MORE INFORMATION

Citation

SNAP predicts effect of mutations on protein function.
Bromberg Y, Yachdav G, Rost B.
Bioinformatics. 2008 Oct 15;24(20):2397-8. Epub 2008 Aug 30.

Strut 0.1 – Protein Function Prediction

Strut 0.1

:: DESCRIPTION

Strut is a C++ package for structured large-margin classification that is designed for hierarchical classification problems such as protein function prediction.

::DEVELOPER

Asa Ben-Hur

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows /MacOsX
C++ Compiler

:: DOWNLOAD

Strut

:: MORE INFORMATION