TissueNet v.2 – Human Tissue Protein-protein Interactions

TissueNet v.2

:: DESCRIPTION

The TissueNet database of human tissue PPIs associates each interaction with human tissues that express both pair mates.

::DEVELOPER

Yeger-Lotem Lab

:: SCREENSHOTS

TissueNet

:: REQUIREMENTS

  • Web Browser 

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2013 Jan;41(Database issue):D841-4. doi: 10.1093/nar/gks1198.
The TissueNet database of human tissue protein-protein interactions.
Barshir R, Basha O, Eluk A, Smoly IY, Lan A, Yeger-Lotem E.

iWRAP – Prediction of Cancer-related Protein-protein Interactions

iWRAP

:: DESCRIPTION

iWRAP is a threading program for identifying the putative interface between two protein sequences. iWRAP is based on RAPTOR, which is a single domain threading program. iWRAP considers only the interface of the template to predict interacting residues in a pair of query sequences. iWRAP uses the open-source optimization library (COIN-OR) to minimize the threading energy function.

::DEVELOPER

Raghavendra Hosur (rhosur@mit.edu)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  iWRAP

:: MORE INFORMATION

Citation

J Mol Biol. 2011 Feb 4;405(5):1295-310. doi: 10.1016/j.jmb.2010.11.025.
iWRAP: An interface threading approach with application to prediction of cancer-related protein-protein interactions.
Hosur R, Xu J, Bienkowska J, Berger B.

IPPI – Inferring Protein-Protein Interactions for YEAST

IPPI

:: DESCRIPTION

IPPI is a web server of inferring protein-protein interactions

::DEVELOPER

Akutsu Laboratory (Laboratory of Mathematical Bioinformatics)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Bioinformatics. 2003 Oct;19 Suppl 2:ii58-65.
Inferring strengths of protein-protein interactions from experimental data using linear programming.
Hayashida M, Ueda N, Akutsu T.

go2ppi 1.06 – Prediction of Protein-protein Interactions

go2ppi 1.06

:: DESCRIPTION

go2ppi is a predictor for protein-protein interactions (PPI) based on Gene Ontology (GO) annotations.

::DEVELOPER

go2ppi team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java

:: DOWNLOAD

  go2ppi

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Jan 1;28(1):69-75. doi: 10.1093/bioinformatics/btr610.
Gene Ontology-driven inference of protein-protein interactions using inducers.
Maetschke SR, Simonsen M, Davis MJ, Ragan MA.

pdCSM-PPI – Using Graph-Based Signatures to Identify Protein-Protein Interaction Inhibitors

pdCSM-PPI

:: DESCRIPTION

pdCSM-PPI is a machine learning approach that uses a graph-based representation of small molecules to guide identification of inhibitors modulating protein-protein interactions.

::DEVELOPER

Biosig Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Rodrigues CHM, Pires DEV, Ascher DB.
pdCSM-PPI: Using Graph-Based Signatures to Identify Protein-Protein Interaction Inhibitors.
J Chem Inf Model. 2021 Nov 22;61(11):5438-5445. doi: 10.1021/acs.jcim.1c01135. Epub 2021 Nov 1. PMID: 34719929.

PPIP – Protein-Protein Interaction Predictor

PPIP

:: DESCRIPTION

The tool PPIP was developed based on the interolog method. Once the user uploads at least two protein sequences in FASTA format into the text area, or a sequence file less than 2 Mb, the corresponding orthologous protein pairs, whose interaction has been verified by biochemical experiments in the selected model organism, will be retrieved.

::DEVELOPER

Huaqin He’s Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

BMC Genomics. 2014 May 7;15:344. doi: 10.1186/1471-2164-15-344.
Genome-wide identification of heat shock proteins (Hsps) and Hsp interactors in rice: Hsp70s as a case study.
Wang Y, Lin S, Song Q, Li K, Tao H, Huang J, Chen X, Que S, He H

iBRET – High Confidence Detection of Protein-protein Interactions in Living Cells

iBRET

:: DESCRIPTION

iBRET is an automated informatics-aided and bioluminescence resonance energy transfer based method enabling high-throughput detection of interactions in living cells.

::DEVELOPER

Institute for Bioinformatics, Ludwig-Maximilians-Universität München

:: SCREENSHOTS

iBRET

:: REQUIREMENTS

  • Linux/ MacOsX / Windows
  • Java

:: DOWNLOAD

 iBRET

:: MORE INFORMATION

pyDockSAXS – Protein-protein Interactions using SAXS and Computational Docking

pyDockSAXS

:: DESCRIPTION

pyDockSAXS server is a web server for rigid-body protein-protein docking that combines computational and experimental information.

::DEVELOPER

pyDockSAXS team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

pyDockSAXS: protein-protein complex structure by SAXS and computational docking.
Jiménez-García B, Pons C, Svergun DI, Bernadó P, Fernández-Recio J.
Nucleic Acids Res. 2015 Apr 20. pii: gkv368.

PSOPIA 20130501 – Prediction Server of Protein-Protein Interactions

PSOPIA 20130501

:: DESCRIPTION

PSOPIA (Prediction Server Of Protein-protein InterActions) is an AODE for predicting protein-protein interactions using three seqeucne based features; (I) sequence similarities to a known interacting protein pair, (II) statistical propensities of domain pairs observed in interacting proteins and (III) a sum of edge weights along the shortest path between homologous proteins in a PPI network.

::DEVELOPER

the Mizuguchi Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2014 Jun 23;15:213. doi: 10.1186/1471-2105-15-213.
Homology-based prediction of interactions between proteins using Averaged One-Dependence Estimators.
Murakami Y, Mizuguchi K.

DeterminePPI 1.0 – Inferring Protein-protein Interactions by Parsimony Principle

DeterminePPI 1.0

:: DESCRIPTION

DeterminePPI aims to infer protein-protein interaction by parsimony principle. Specifically, inferring domain interactions is formulated as an integer linear programming and solved by relaxed linear programming. In contrast to probabilistic algorithms, DeterminePPI is an algorithm based on a deterministic model.

::DEVELOPER

APORC

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

  DeterminePPI

:: MORE INFORMATION

Citation

Chen C, Zhao JF, Huang Q, Wang RS, Zhang XS.
Inferring domain-domain interactions from protein-protein interactions in the complex network conformation.
BMC Syst Biol. 2012;6 Suppl 1:S7. doi: 10.1186/1752-0509-6-S1-S7.