PCP 1.0 – Protein Complex Prediction

PCP 1.0

:: DESCRIPTION

PCP is a sofware that searches for cliques in the modified network, and merge cliques to form clusters using a “partial clique merging” method. Experiments show that (1) the use of indirect interactions and topological weight to augment protein-protein interactions can be used to improve the precision of clusters predicted by various existing clustering algorithms; and (2) our complex-finding algorithm performs very well on interaction networks modified in this way. Since no other information except the original PPI network is used, the would be very useful for protein complex prediction, especially for prediction of novel protein complexes.

::DEVELOPER

Limsoon Wong Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  •  Linux
  • C++ Compiler
  • Perl

:: DOWNLOAD

 PCP

:: MORE INFORMATION

Citation:

J Bioinform Comput Biol. 2008 Jun;6(3):435-66.
Using indirect protein-protein interactions for protein complex prediction.
Chua HN, Ning K, Sung WK, Leong HW, Wong L.

DockStar – Modelling of multimolecular Protein Complexes

DockStar

:: DESCRIPTION

DockStar is an algorithm for modeling of multimolecular protein complexes. It integrates both high resolution data of the individual subunits and low resolution data, such as the complex interaction graph and chemical cross-links.

::DEVELOPER

 the BioInfo3D group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

DockStar: a Novel ILP based Integrative Method for Structural Modeling of Multimolecular Protein Complexes.
Amir N, Cohen D, Wolfson H.
Bioinformatics. 2015 Apr 25. pii: btv270.

Pepper 1.5.1 – Protein Complex Expansion using Protein-Protein intERaction networks

Pepper 1.5.1

:: DESCRIPTION

PEPPER is a plugin which finds meaningful pathways / complexes connecting a protein set members within a PPI-network using multi-objective optimization.

::DEVELOPER

iSSB – Institute of Systems & Synthetic Biology

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java
  • CytoScape

:: DOWNLOAD

 Pepper

:: MORE INFORMATION

Citation

Pepper: Cytoscape app for Protein complex Expansion using Protein-Protein intERaction networks.
Winterhalter C, Nicolle R, Louis A, To C, Radvanyi F, Elati M.
Bioinformatics. 2014 Aug 18. pii: btu517

CACHET – Discovery of Protein Complexes with Core-Attachment Structures from TAP Data

CACHET

:: DESCRIPTION

CACHET is a method that detects protein complexes with Core-AttaCHment structures directly from bipartitETAP data.

::DEVELOPER

Xiaoli Li, PhD

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  •  Windows

:: DOWNLOAD

 CACHET

:: MORE INFORMATION

Citation

J Comput Biol. 2012 Sep;19(9):1027-42. doi: 10.1089/cmb.2010.0293. Epub 2011 Jul 21.
Discovery of protein complexes with core-attachment structures from Tandem Affinity Purification (TAP) data.
Wu M1, Li XL, Kwoh CK, Ng SK, Wong L.

DDNA 3.1 – DNA/Protein Complex Interaction Energy

DDNA 3.1

:: DESCRIPTION

DDNA is a software for interaction energy between protein and DNA

::DEVELOPER

Laboratory of Structural Bioinformatics and Design

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 DDNA

 :: MORE INFORMATION

Citation

Bioinformatics. 2010 Aug 1;26(15):1857-63. doi: 10.1093/bioinformatics/btq295. Epub 2010 Jun 4.
Structure-based prediction of DNA-binding proteins by structural alignment and a volume-fraction corrected DFIRE-based energy function.
Zhao H1, Yang Y, Zhou Y.

Spotlight – Assembly of Protein Complex from Interactomes

Spotlight

:: DESCRIPTION

Spotlight Web Service is designed to detect community structures in a network. Community, in which vertices are joined tightly together, between which there are only looser edges, exists in many real networks. Detecting community in a network is a very important research topic, because it has many practical applications. For example, detecting communities can help us find out real social groupings in a social network, related papers on a single topic in a citation network, protein complexes in Protein-Protein Interaction network, and web pages on related topics in the World Wide Web.

::DEVELOPER

Laboratory of Systems Biology and Network Biology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Spotlight: assembly of protein complexes by integrating graph clustering methods.
Chin CH, Chen SH, Chen CY, Hsiung CA, Ho CW, Ko MT, Lin CY.
Gene. 2013 Apr 10;518(1):42-51. doi: 10.1016/j.gene.2012.11.087

MCL_CAw – Refinement of MCL for Protein Complex Detection

MCL_CAw

:: DESCRIPTION

MCL-CAw is a refinement of MCL for detecting yeast complexes from weighted PPI networks by incorporating core-attachment structure

::DEVELOPER

MCL_CAw team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/  Windows /macOsX
  • C/C++ Compiler

:: DOWNLOAD

 MCL-CAw

:: MORE INFORMATION

Citation

Srihari S, Ning K, Leong HW (2010).
MCL-CAw: a refinement of MCL for detecting yeast complexes from weighted PPI networks by incorporating core-attachment structure,
BMC Bioinformatics, 11:504.

Core 0.10 – Predict Protein Complex from PPI network

Core 0.10

:: DESCRIPTION

Core is an open source program for predicting protein complex from PPI network.

::DEVELOPER

Bioinformatics Research Group of Hong Kong University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Core

:: MORE INFORMATION

Citation:

Predicting protein complexes from PPI data: a core-attachment approach.
Leung HC, Xiang Q, Yiu SM, Chin FY.
J Comput Biol. 2009 Feb;16(2):133-44.

 

ProCope 1.2 – Protein Complex Prediction and Evaluation

ProCope 1.2

:: DESCRIPTION

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. Methods can be accessed via a graphical user interface, command line tools and a Java API. Using ProCope, existing algorithms can be applied quickly and reproducibly on new experimental results, individual steps of the different algorithms can be combined in new and innovative ways and new methods can be implemented and integrated in the existing prediction framework.

::DEVELOPER

Institut für Informatik, Ludwig-Maximilians-Universität München

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / MacOSX
  • Java

:: DOWNLOAD

ProCope

:: MORE INFORMATION

Citation

Jan Krumsiek, Caroline C. Friedel, Ralf Zimmer.
ProCope–protein complex prediction and evaluation.
Bioinformatics, vol 24, no. 18, pp. 2115–2116, Sep 2008.