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ProCope specifications

Information


Unique identifier OMICS_26382
Name ProCope
Alternative name Protein complex Prediction and Evaluation
Software type Package/Module, Toolkit/Suite
Interface Command line interface, Graphical user interface, Application programming interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Java
License GNU Lesser General Public License version 3.0
Computer skills Advanced
Version 1.2
Stability Stable
Requirements
Java Runtime Environment
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Caroline C Friedel

Additional information


https://www.bio.ifi.lmu.de/files/Software/procope/doc/index.html

Publication for Protein complex Prediction and Evaluation

ProCope citations

 (18)
library_books

A two step framework for inferring direct protein protein interaction network from AP MS data

2017
BMC Syst Biol
PMCID: 5615237
PMID: 28950876
DOI: 10.1186/s12918-017-0452-y

[…] he experiments, we use SA, PE, Hart and DC methods as the scoring methods in the first phase to construct an initial PPI network. All the interaction scores for each algorithm are generated using the ProCope software [] (https://drupal.bio.ifi.lmu.de/Complexes/ProCope/) with the default parameter settings. To obtain a filtered network in the second phase, we use the network deconvolution (ND) meth […]

library_books

Dynamic stepwise opening of integron attC DNA hairpins by SSB prevents toxicity and ensures functionality

2017
Nucleic Acids Res
PMCID: 5737091
PMID: 28985409
DOI: 10.1093/nar/gkx670

[…] German Federal Ministry of Education and Research [BMBF 03Z2EN11 to M.S.]; Franco-German PROCOPE program of the German Academic exchange service [DAAD 55931827 to M.S.]; French Ministry of Foreign Affairs [PHC 28351PC to D.M.]; Dresden International Graduate School for Biomedicine and Bio […]

library_books

Near Infrared Spectroscopy – Electroencephalography Based Brain State Dependent Electrotherapy: A Computational Approach Based on Excitation–Inhibition Balance Hypothesis

2016
PMCID: 4976097
PMID: 27551273
DOI: 10.3389/fneur.2016.00123

[…] Research was conducted within the context of the regional NUMEV funding, Franco-German PHC-PROCOPE 2014 funding, and Franco-Indian INRIA-DST funding. This research was funded by D.R. Ramalingaswami fellowship (BT/RLF/Re-entry/07/2014) from the Department of Biotechnology, Ministry of Scienc […]

library_books

Dynamic identifying protein functional modules based on adaptive density modularity in protein protein interaction networks

2015
BMC Bioinformatics
PMCID: 4705501
PMID: 26330105
DOI: 10.1186/1471-2105-16-S12-S5

[…] larity is, the greater the probability that the proteins perform similar biological functions.It is convenient for us to calculate the GO semantic similarity of protein functional modules by the tool ProCope []. Owing to the poor performance of MCODE algorithm in the above section, here we evaluate the performance of ADM algorithm in terms of GO semantic similarity by comparing it to MCL and Clust […]

library_books

An efficient protein complex mining algorithm based on Multistage Kernel Extension

2014
BMC Bioinformatics
PMCID: 4255745
PMID: 25474367
DOI: 10.1186/1471-2105-15-S12-S7

[…] positioning in the same cellular compartment indicates the stronger recognition capability of the algorithm. This paper adopts the genome co-localization reference dataset from literature [] and the ProCope [] tool to analyze the GO semantic similarity and co-localization enrichment on the results predicted by each algorithm on Krogan and Collins dataset.In the Table the figures of Reference dat […]

library_books

A Novel Algorithm for Detecting Protein Complexes with the Breadth First Search

2014
Biomed Res Int
PMCID: 4003846
PMID: 24818139
DOI: 10.1155/2014/354539

[…] localized []. Generally, higher coannotation and colocalization scores [] show that proteins within the same protein complexes tend to share higher functional similarity. We employ the software suite ProCope (http://www.bio.ifi.lmu.de/Complexes/ProCope/) to compute the colocalization and coannotation scores in our experiment. […]

Citations

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ProCope institution(s)
Institut fur Informatik, Ludwig-Maximilians-Universität München, Munchen, Germany

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