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Methods for protein complex prediction and their contributions towards understanding the 
organisation, function and dynamics of complexes
Sriganesh Srihari1, Chern Han Yong2, Ashwini Patil3 and Limsoon Wong2
1Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland 4067, Australia
2Department of Computer Science, National University of Singapore, Singapore 117417, Singapore
3Human Genome Centre, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan


Citation

Srihari S, Yong CH, Patil A, Wong L (2015). Methods for protein complex prediction and their contributions towards understanding the organisation, function and dynamics of complexes, FEBS Letters doi:10.1016/j.febslet.2015.04.026[PDF] with [Slides!]

Download datasets used in the paper [ZIP]


Table 1: Methods for protein complex prediction from protein interaction networks. Associated softwares are available as Cytoscape [40] plug-ins (Cy), command line programs (CL) or as online (OL) web servers under the mentioned links. (Please see the paper for the cited references)

Classification

Method

Availability (URL)

Reference

 

MCODE (Cy)

http://apps.cytoscape.org/apps/mcode

[12]

 

MCL (Cy, CL)

http://micans.org/mcl/

http://apps.cytoscape.org/apps/clustermaker

 

[41-43]

Solely

network clustering

CMC (CL)

https://www.comp.nus.edu.sg/~wongls/projects/complexprediction/CMC-26may09/

[45]

 

ClusterONE (Cy)

http://apps.cytoscape.org/apps/clusterone

[49]

 

HACO (CL)

http://www.bio.ifi.lmu.de/Complexes/ProCope/

[44,50]

 

PPSampler (CL)

http://imi.kyushu-u.ac.jp/~om/PPSamplerVer1.2/PPSamplerVer1_2.exe

[72]

 

CORE (CL)

http://alse.cs.hku.hk/complexes/

[54]

Core-attachment structure

COACH (CL)

http://www1.i2r.a-star.edu.sg/~xlli/coach.zip

[55]

 

MCL-CAw (CL)

https://sites.google.com/site/mclcaw/

[56,57]

Functional information

RNSC (CL)

http://www.cs.utoronto.ca/~juris/data/ppi04/

[59]

 

PCP (CL)

https://www.comp.nus.edu.sg/~wongls/projects/complexprediction/PCP-3aug07/

[61]

 

NetworkBLAST (OL)

http://www.cs.tau.ac.il/~bnet/networkblast.htm

[79,149]

Evolutionary information

NetworkBLAST-M (CL)

http://www.cs.tau.ac.il/~bnet/License-nbm.htm

[79,149]

 

COCIN (CL)

https://sites.google.com/site/cocinhy/

[36]

Mutual exclusive interactions

SPIN (CL)

https://code.google.com/p/simultaneous-pin/

[68]

 

DACO (CL)

http://sourceforge.net/projects/dacoalgorithm/

[70]

Sparse complexes

SWC (CL)

http://www.comp.nus.edu.sg/~wongls/projects/complexprediction/SWC-31oct14

[53]

Small complexes

SSS (CL)

http://www.comp.nus.edu.sg/~wongls/projects/complexprediction/sss-3dec2014.zip

[75]

Temporal complexes

TS-OCD (CL)

http://mail.sysu.edu.cn/home/stsddq@mail.sysu.edu.cn/dai/others/TSOCD.zip

[99]

Complexes in diseases

CONTOUR (CL)

https://sites.google.com/site/contourv1/

[39]


Contact: sriganesh [dot] m [dot] s [at] gmail [dot] com

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