PPIevo – Protein-protein Interaction Prediction from PSSM based Evolutionary Information

PPIevo

:: DESCRIPTION

PPIevo is a software of protein-protein interaction prediction from PSSM based evolutionary information

::DEVELOPER

Laboratory of Systems Biology & Bioinformatics (LBB)

:: SCREENSHOTS

PPIevo

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • Java

:: DOWNLOAD

 PPIevo

:: MORE INFORMATION

Citation:

Genomics. 2013 Oct;102(4):237-42. doi: 10.1016/j.ygeno.2013.05.006. Epub 2013 Jun 6.
PPIevo: protein-protein interaction prediction from PSSM based evolutionary information.
Zahiri J1, Yaghoubi O, Mohammad-Noori M, Ebrahimpour R, Masoudi-Nejad A.

LocFuse – Human protein-protein Interaction Prediction

LocFuse

:: DESCRIPTION

LocFuse is a novel ensemble learning method of human protein-protein interaction prediction via classifier fusion using protein localization information.

::DEVELOPER

Laboratory of Systems Biology & Bioinformatics (LBB)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux
  • JRE

:: DOWNLOAD

 LocFuse

:: MORE INFORMATION

Citation

LocFuse: human protein-protein interaction prediction via classifier fusion using protein localization information.
Zahiri J, Mohammad-Noori M, Ebrahimpour R, Saadat S, Bozorgmehr JH, Goldberg T, Masoudi-Nejad A.
Genomics. 2014 Dec;104(6 Pt B):496-503. doi: 10.1016/j.ygeno.2014.10.006.

MetaPred2CS 1.1 – Meta-predictor for Protein-protein Interactions of Prokaryotic Two-component System Proteins

MetaPred2CS 1.1

:: DESCRIPTION

MetaPred2CS Web server is a meta-predictor based on Support Vector Machine (SVM) that combines 6 individual sequence based protein-protein interaction prediction methods to predict prokaryotic two-component system protein-protein interactions (PPIs).

::DEVELOPER

Bioinformatics @ IBERS

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 MetaPred2CS

:: MORE INFORMATION

Citation

Bioinformatics. 2016 Jul 4. pii: btw403.
MetaPred2CS: a sequence-based meta-predictor for protein-protein interactions of prokaryotic two-component system proteins.
Kara A, Vickers M, Swain M, Whitworth DE, Fernandez-Fuentes N.

PRISM 2.0 – Prediction of Protein-protein Interactions and Modeling their 3D Complexes

PRISM 2.0

:: DESCRIPTION

The PRISM web server enables fast and accurate prediction of protein-protein interactions (PPIs).

::DEVELOPER

the COSBI (Computational Systems Biology) group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

PRISM PROTOCOL

:: MORE INFORMATION

Citation

Baspinar A, Cukuroglu E, Nussinov R, Keskin O, Gursoy A.
PRISM: A web server and repository for prediction of protein-protein interactions and modeling their 3D complexes.
Nucl. Acids Res. (2014) doi: 10.1093/nar/gku397

Struct2Net – Structure-based Computational Predictions of Protein-protein interactions

Struct2Net

:: DESCRIPTION

The Struct2Net program predicts protein-protein interactions (PPI) by integrating structure-based information with other functional annotations, e.g. GO, co-expression and co-localization etc. The structure-based protein interaction prediction is conducted using a protein threading server RAPTOR plus logistic regression.

::DEVELOPER

Berger Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • WebServer

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Struct2Net: a web service to predict protein-protein interactions using a structure-based approach.
Singh R, Park D, Xu J, Hosur R, Berger B.
Nucleic Acids Res. 2010 Jul;38(Web Server issue):W508-15. doi: 10.1093/nar/gkq481

DeNovo – Virus-Host Sequence-Based Protein-Protein Interaction Prediction

DeNovo

:: DESCRIPTION

DeNovo is a sequence-based negative sampling and machine learning framework that learns from PPIs of different viruses to predict for a novel one, exploiting the shared host proteins.

::DEVELOPER

Fatma Elzahraa S. Eid

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • MatLab

:: DOWNLOAD

 DeNovo

:: MORE INFORMATION

Citation

DeNovo: Virus-Host Sequence-Based Protein-Protein Interaction Prediction.
Eid FE, ElHefnawi M, Heath LS.
Bioinformatics. 2015 Dec 16. pii: btv737.

DynaFace – Discrimination between Obligatory and Non-obligatory Protein-Protein Interactions

DynaFace

:: DESCRIPTION

DynaFace predicts obligatory and non-obligatory interactions among a set of 300 putative protein complexes.

::DEVELOPER

Polymer Research Center

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser
:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

DynaFace: Discrimination between Obligatory and Non-obligatory Protein-Protein Interactions Based on the Complex’s Dynamics.
Soner S, Ozbek P, Garzon JI, Ben-Tal N, Haliloglu T.
PLoS Comput Biol. 2015 Oct 27;11(10):e1004461. doi: 10.1371/journal.pcbi.1004461.

ppiPre 1.9 – Predict Protein-Protein Interactions Based on Functional and Topological Similarities

ppiPre 1.9

:: DESCRIPTION

ppiPre is an open-source framework for PPI analysis and prediction using a combination of heterogeneous features including three GO-based semantic similarities, one KEGG-based co-pathway similarity and three topology-based similarities.

::DEVELOPER

Yue Deng <anfdeng at 163.com>, Rongjie Shao, Gang Wang and Yuanjun Sun

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX / Windows
  • R
  • BioConductor

:: DOWNLOAD

 ppiPre

:: MORE INFORMATION

Citation

BMC Syst Biol. 2013;7 Suppl 2:S8. doi: 10.1186/1752-0509-7-S2-S8. Epub 2013 Oct 14.
ppiPre: predicting protein-protein interactions by combining heterogeneous features.
Deng Y, Gao L, Wang B.

Profppikernel 1.0.4 – Protein-protein Interaction Prediction

Profppikernel 1.0.4

:: DESCRIPTION

Profppikernel uses an accelerated version of the original profile kernel to train SVM based protein-protein interaction (PPI) prediction models and to predict new PPIs from sequence alone.

::DEVELOPER

Rost Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Profppikernel

:: MORE INFORMATION

Citation

Evolutionary profiles improve protein-protein interaction prediction from sequence.
Hamp T, Rost B.
Bioinformatics. 2015 Feb 4. pii: btv077.

HIPPIE 1.7 – study and filter the Network of Human Protein-protein Interaction data

HIPPIE 1.7

:: DESCRIPTION

HIPPIE (Human Integrated Protein-Protein Interaction rEference) is a human PPI dataset with a normalized scoring scheme that integrates multiple experimental PPI datasets.

::DEVELOPER

Computational Biology and Data Mining Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java

:: DOWNLOAD

 HIPPIE

:: MORE INFORMATION

Citation

PLoS One. 2012;7(2):e31826. doi: 10.1371/journal.pone.0031826. Epub 2012 Feb 14.
HIPPIE: Integrating protein interaction networks with experiment based quality scores.
Schaefer MH1, Fontaine JF, Vinayagam A, Porras P, Wanker EE, Andrade-Navarro MA.