PDZPepInt 1.0.0 – PDZ-peptide Interaction prediction

PDZPepInt 1.0.0

:: DESCRIPTION

PDZPepInt is a cluster based prediction tool to predict binding peptides of PDZ domains in human, mouse, fly and worm. Total 43 built-in models that cover 226 PDZ domains across the species are available. Peptides are represented as 5 C-terminal sequences of binding proteins. Depending on the user requirement Gene Ontology database can be used for getting reliable interactions. Additionally, it will also consider the C-terminal peptides that are intrinsically unstructured for getting high confidence interactions.

::DEVELOPER

Chair for Bioinformatics Freiburg

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BMC Genomics. 2014;15 Suppl 1:S5. doi: 10.1186/1471-2164-15-S1-S5. Epub 2014 Jan 24.
Cluster based prediction of PDZ-peptide interactions.
Kundu K, Backofen R.

HubPredictor v1.0 beta – Predicting Chromatin Interaction Hubs using Histone Marks information

HubPredictor v1.0 beta

:: DESCRIPTION

HubPredictor is the R function to run Bayesian Additive Regression Trees (BART) model for predicting chromatin interaction hubs using histone marks information.

::DEVELOPER

Guo-CHeng Yuan Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • R

:: DOWNLOAD

HubPredictor

:: MORE INFORMATION

Citation

Genome Biol, 16 (1), 162 2015 Aug 14
Predicting Chromatin Organization Using Histone Marks
Jialiang Huang , Eugenio Marco , Luca Pinello , Guo-Cheng Yuan

EPIP – Condition-specific Enhancer–promoter Interaction prediction

EPIP

:: DESCRIPTION

EPIP is a software used to identify target genes of enhancers in human genome. It is a novel computational method to reliably predict EPIs, especially condition-specific ones. EPIP is capable of predicting interactions in samples with limited data as well as in samples with abundant data.

::DEVELOPER

Hu Lab – Data Integration and Knowledge Discovery @ UCF

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • Python

:: DOWNLOAD

EPIP

:: MORE INFORMATION

Citation:

Bioinformatics. 2019 Oct 15;35(20):3877-3883. doi: 10.1093/bioinformatics/btz641.
EPIP: a novel approach for condition-specific enhancer-promoter interaction prediction.
Talukder A, Saadat S, Li X, Hu H.

Hi-Jack – Pathway-based Inference of Host-pathogen Interactions

Hi-Jack

:: DESCRIPTION

Hi-Jack, a novel computational framework, for inferring pathway-based interactions between a host and a pathogen that relies on the idea of metabolite hijacking.

::DEVELOPER

InfoCloud Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / MacOsX / Linux
  • C++ Compiler

:: DOWNLOAD

Hi-Jack

:: MORE INFORMATION

Citation:

Hi-Jack: A novel computational framework for pathway-based inference of host-pathogen interactions.
Kleftogiannis D, Wong L, Archer JA, Kalnis P.
Bioinformatics. 2015 Mar 9. pii: btv138

INTERSPIA – INTER-Species Protein Interaction Analysis

INTERSPIA

:: DESCRIPTION

INTERSPIA is a web-based application for the analysis and visualization of the dynamics of protein-protein interactions among multiple species.

::DEVELOPER

Bioinformatics Laboratory, Konkuk University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

INTERSPIA: a web application for exploring the dynamics of protein-protein interactions among multiple species.
Kwon D, Lee D, Kim J, Lee J, Sim M, Kim J.
Nucleic Acids Res. 2018 Jul 2;46(W1):W89-W94. doi: 10.1093/nar/gky378.

PEP – Predict Enhancer Promoter interactions

PEP

:: DESCRIPTION

PEP is a framework for predicting long-range enhancer-promoter interactions (EPI) incorporating two strategies for extracting features directly from the DNA sequences of enhancer and promoter elements

::DEVELOPER

Ma Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Python

:: DOWNLOAD

PEP

:: MORE INFORMATION

Citation

Exploiting sequence-based features for predicting enhancer-promoter interactions.
Yang Y, Zhang R, Singh S, Ma J.
Bioinformatics. 2017 Jul 15;33(14):i252-i260. doi: 10.1093/bioinformatics/btx257

DT-Hybrid 0.99.2 – Drug-target Interaction Prediction

DT-Hybrid 0.99.2

:: DESCRIPTION

DT-Hybrid is an R package that implements the homonymous algorithm for the prediction of interactions between small-molecules (i.e. Drug-Target Interactions).

::DEVELOPER

DT-Hybrid team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / WIndows/ MacOsX
  • R

:: DOWNLOAD

 DT-Hybrid

:: MORE INFORMATION

Citation:

Drug-target interaction prediction through domain-tuned network-based inference.
Alaimo S, Pulvirenti A, Giugno R, Ferro A.
Bioinformatics. 2013 Aug 15;29(16):2004-8. doi: 10.1093/bioinformatics/btt307.

POW – PDZ Domain-peptide Interaction Prediction

POW

:: DESCRIPTION

POW is a website that allows users to predict PDZ domain-peptide interactions for human, mouse, worm and fly PDZ domains.

::DEVELOPER

Bader Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2013 Jan 21;14:27. doi: 10.1186/1471-2105-14-27.
Predicting PDZ domain mediated protein interactions from structure.
Hui S1, Xing X, Bader GD.

DoMo-Pred – Domain-Motif Mediated Interaction Prediction

DoMo-Pred

:: DESCRIPTION

DoMo-Pred is a Domain-Motif Mediated Interaction Prediction command line tool

::DEVELOPER

Bader Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux
  • Python

:: DOWNLOAD

 DoMo-Pred

:: MORE INFORMATION

Citation:

Predicting physiologically relevant SH3 domain mediated protein-protein interactions in yeast.
Jain S, Bader GD.
Bioinformatics. 2016 Feb 9. pii: btw045.