ProCope - Protein Complex Prediction and Evaluation

ProCope is a software package which provides easy access to different methods used for the prediction and evaluation of protein complexes from purification data experiments.

Large scale protein purification experiments provide a vast amount of indirect protein-protein interaction information. As these data are inherently noisy and incomplete, sophisticated methods are required to predict actual protein complexes existing and operating in-vivo. Since the publication of two large-scale purification datasets for the yeast Saccharomyces cerevisiae in 2006 (Gavin et al. and Krogan et al.) different methods for the processing of these datasets have been developed. These include methods for the derivation of PPI score networks from the data, the clustering of these networks to predict actual complexes and the evaluation of the predictions using experimental data.

ProCope implements many of the methods described in the literature along with further useful methods for PPI score network manipluation, complex set manipulation, data integration with Petri nets and result visualization. All functionality can be accessed using a graphical user interface, a collection of command line tools and an application programming interface (API) to use all these features in your own computer programs. The whole software package is written in Java and requires the Java Runtime Environment 5.0 or higher.

Getting started

Installation guide

If you quickly want to start using ProCope check out the first steps guide of the graphical user interface.

Parts of the package

Detailed documentations of the three differents parts of the package are linked here and above in the navigation panel.

Methods and Materials

Here you find information about the datasets and methods implemented in the package and references to the original literature. Note the navigation panel on the left which gives you quick access to all parts of this documentation.

Additional information and features

ProCope documentation