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

Struct2Net 1.0

:: 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

  • Linux

:: DOWNLOAD

Struct2Net

:: 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

Coev2Net – Boosting Confidence in High-throughput Protein-protein Interaction datasets

Coev2Net

:: DESCRIPTION

Coev2Net is a general framework to predict, assess and boost confidence in individual interactions inferred from a HTP experiment. For every pair of interaction in the HTP screen, Coev2Net provides a score to assess their likelihood of being co-evolved from interacting homologous sequences.

::DEVELOPER

Bonnie Berger‘s group at MIT.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Perl

:: DOWNLOAD

 Coev2Net

:: MORE INFORMATION

Citation:

Genome Biol. 2012 Aug 31;13(8):R76.
A computational framework for boosting confidence in high-throughput protein-protein interaction datasets.
Hosur R, Peng J, Vinayagam A, Stelzl U, Xu J, Perrimon N, Bienkowska J, Berger B.

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.

iLoops – Protein-protein Interaction prediction server based on Structural Features

iLoops

:: DESCRIPTION

The iLoops Server uses the loop classification as defined in ArchDB and/or the SCOP classification of domains to predict whether or not a pair of proteins interact.

::DEVELOPER

Structural BioInformatics Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Sep 15;29(18):2360-2. doi: 10.1093/bioinformatics/btt401. Epub 2013 Jul 9.
iLoops: a protein-protein interaction prediction server based on structural features.
Planas-Iglesias J1, Marin-Lopez MA, Bonet J, Garcia-Garcia J, Oliva B.

HIPPIE 2.2 – study and filter the Network of Human Protein-protein Interaction data

HIPPIE 2.2

:: 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 (CBDM) Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java

:: DOWNLOAD

 HIPPIE

:: MORE INFORMATION

Citation

HIPPIE v2.0: enhancing meaningfulness and reliability of protein-protein interaction networks.
Alanis-Lobato G, Andrade-Navarro MA, Schaefer MH.
Nucleic Acids Res. 2017 Jan 4;45(D1):D408-D414. doi: 10.1093/nar/gkw985

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.

PIPs 1.1 – Human Protein-Protein Interaction Predictions

PIPs 1.1

:: DESCRIPTION

PIPs is a database of predicted human protein-protein interactions. The predictions have been made using a na?ve Bayesian classifier to calculate a Score of interaction.

::DEVELOPER

The Barton Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

 NO

:: MORE INFORMATION

Citation

PIPs: human protein–protein interaction prediction database
Mark D. McDowall, Michelle S. Scott and Geoffrey J. Barton
Nucl. Acids Res. (2009) 37 (suppl 1): D651-D656. doi: 10.1093/nar/gkn870

MEGADOCK 4.1.1 / MEGADOCK-K 3.0 / MEGADOCK-GPU 1.0 – Protein-protein Interaction Prediction System

MEGADOCK 4.1.1 / MEGADOCK-K 3.0 / MEGADOCK-GPU 1.0

:: DESCRIPTION

MEGADOCK is an fft-based protein-protein docking system for all-to-all protein-protein interaction predictions.

MEGADOCK-K is an MEGADOCK on K computer

MEGADOCK-GPU is an ultra-fast protein-protein docking software on GPUs.

::DEVELOPER

Akiyama Laboratory, Tokyo Institute of Technology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler
  • FFTW3
:: DOWNLOAD

  MEGADOCK / MEGADOCK-K/ MEGADOCK-GPU

:: MORE INFORMATION

Citation

MEGADOCK 4.0: an ultra-high-performance protein-protein docking software for heterogeneous supercomputers.
Ohue M, Shimoda T, Suzuki S, Matsuzaki Y, Ishida T, Akiyama Y.
Bioinformatics. 2014 Aug 6. pii: btu532.

MEGADOCK 3.0: a high-performance protein-protein interaction prediction software using hybrid parallel computing for petascale supercomputing environments.
Matsuzaki Y, Uchikoga N, Ohue M, Shimoda T, Sato T, Ishida T, Akiyama Y.
Source Code Biol Med. 2013 Sep 3;8(1):18

MEGADOCK: An All-to-all Protein-protein Interaction Prediction System Using Tertiary Structure Data.
Ohue M, Matsuzaki Y, Uchikoga N, Ishida T, Akiyama Y.
Protein Pept Lett. 2013 Jul 9

Takehiro Shimoda, Takashi Ishida, Shuji Suzuki, Masahito Ohue, Yutaka Akiyama.
MEGADOCK-GPU: An accelerated protein-protein docking calculation on GPUs,
Parallel and Cloud-based Bioinformatics and Biomedicine, 2013. (accepted)

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.

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.