Tag: Interaction

GenomicInteractions 1.26.0 – Exploring Chromatin interaction data

GenomicInteractions 1.26.0

:: DESCRIPTION

GenomicInteractions is an R/Bioconductor package for manipulating and investigating chromatin interaction data.

::DEVELOPER

Computational Regulatory Genomics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows  / MacOsX
  • R/Bioconductor

:: DOWNLOAD

GenomicInteractions

:: MORE INFORMATION

Citation:

Harmston N, Ing-Simmons E, Perry M, Barešić A, Lenhard B.
GenomicInteractions: An R/Bioconductor package for manipulating and investigating chromatin interaction data.
BMC Genomics. 2015 Nov 17;16:963. doi: 10.1186/s12864-015-2140-x. PMID: 26576536; PMCID: PMC4650858.

PLIC – Protein-ligand Interaction Clusters

PLIC

:: DESCRIPTION

PLIC is a database of protein-ligand interaction clusters.

::DEVELOPER

Chandra lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation

Anand P, Nagarajan D, Mukherjee S, Chandra N.
PLIC: protein-ligand interaction clusters.
Database (Oxford). 2014 Apr 23;2014(0):bau029. doi: 10.1093/database/bau029. PMID: 24763918; PMCID: PMC3998096.

MTide – Identification of miRNA-target Interaction in Plants

MTide

:: DESCRIPTION

MTide is an integrated tool for the identification of miRNA-target interaction in plants. The core algorithm consists of a modified miRDeep2 and a modified CleaveLand4.

::DEVELOPER

Ming Chen’s Bioinformatics Group, Zhejiang University.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 MTide

:: MORE INFORMATION

Citation

MTide: an integrated tool for the identification of miRNA-target interaction in plants.
Zhang Z, Jiang L, Wang J, Chen M.
Bioinformatics. 2014 Sep 24. pii: btu633.

ScanSite 4.0 – Kinase-substrate Interaction Prediction and Short Linear Sequence Motif Discover

ScanSite 4.0

:: DESCRIPTION

Scansite searches for motifs within proteins that are likely to be phosphorylated by specific protein kinases or bind to domains such as SH2 domains, 14-3-3 domains or PDZ domains.

::DEVELOPER

ScanSite team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Scansite 2.0: Proteome-wide prediction of cell signaling interactions using short sequence motifs.
Obenauer JC, Cantley LC, Yaffe MB.
Nucleic Acids Res. 2003 Jul 1;31(13):3635-41.

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

Genes2Networks 1.5 – Connecting Lists of Gene Symbols using Mammalian Protein Interactions databases

Genes2Networks 1.5

:: DESCRIPTION

Genes2Networks (G2N) is a tool that can be used to place lists of mammalian genes in the context of a background mammalian signalome and interactome networks. The input to the program is a list of human Entrez Gene gene symbols and background networks in SIG format, while the output includes: (a) all identified interactions for the genes/proteins, (b) a subnetwork connecting the genes/proteins using intermediate components that are used to connect the genes, (c) ranking of the specificity of intermediate components to interact with the list of genes/proteins.

::DEVELOPER

Ma’ayan Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX

:: DOWNLOAD

 Genes2Networks

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2007 Oct 4;8:372.
Genes2Networks: connecting lists of gene symbols using mammalian protein interactions databases.
Berger SI, Posner JM, Ma’ayan A.

iPPI-Esml – Identifying Interactions of Proteins

iPPI-Esml

:: DESCRIPTION

iPPI-Esml is an ensemble classifier for identifying the interactions of proteins by incorporating their physicochemical properties and wavelet transforms into PseAAC.

::DEVELOPER

Xiao Lab

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

iPPI-Esml: An ensemble classifier for identifying the interactions of proteins by incorporating their physicochemical properties and wavelet transforms into PseAAC.
Jia J, Liu Z, Xiao X, Liu B, Chou KC.
J Theor Biol. 2015 Apr 20. pii: S0022-5193(15)00173-3. doi: 10.1016/j.jtbi.2015.04.011.

PPI / PPI_RF – Prediction of Protein-Protein Interactions

PPI / PPI_RF

:: DESCRIPTION

The web-server PPI  is used to predict the protein-protein interaction.The protein sequence are represented by chaos game representation and wavelets transform. The chaos game representation encodes the amino acid position of the proteion and then two discrete series are gotten. The wavelets transform is used to analyse the two series. Finally the random forests algorithm is used for PPIs prediction.

The web-server PPI_RF is used to predict the protein-protein interaction. Based on the physicochemical descriptors, a protein could be converted into several digital signals and then wavelet transform was used to analyze them. With such a formulation frame to represent the samples of protein sequences, the random forests algorithm was adopted to conduct prediction.

::DEVELOPER

Xiao Lab

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Prediction of protein-protein interactions using chaos game representation and wavelet transform via the random forest algorithm.
Jia JH, Liu Z, Chen X, Xiao X, Liu BX.
Genet Mol Res. 2015 Oct 2;14(4):11791-805. doi: 10.4238/2015.

Prediction of Protein-Protein Interactions with Physicochemical Descriptors and Wavelet Transform via Random Forests.
Jia J, Xiao X, Liu B.
J Lab Autom. 2015 Apr 16. pii: 2211068215581487

iNR-Drug – Predicting drug-NR interaction in Cellular Networking

iNR-Drug

:: DESCRIPTION

The webserver iNR-Drug was developed for predicting interaction between NRs (Nuclear receptors) and drugs in the cellular networks.

::DEVELOPER

Xiao Lab

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

iNR-Drug: predicting the interaction of drugs with nuclear receptors in cellular networking.
Fan YN, Xiao X, Min JL, Chou KC.
Int J Mol Sci. 2014 Mar 19;15(3):4915-37. doi: 10.3390/ijms15034915.

iGPCR-Drug – Predicting Drug-GPCR Interaction in Cellular Networking

iGPCR-Drug

:: DESCRIPTION

The webserver iGPCR-Drug was developed for predicting interaction between GPCRs and drugs in the cellular networks.

::DEVELOPER

Xiao Lab

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

PLoS One. 2013 Aug 27;8(8):e72234. doi: 10.1371/journal.pone.0072234. eCollection 2013.
iGPCR-drug: a web server for predicting interaction between GPCRs and drugs in cellular networking.
Xiao X1, Min JL, Wang P, Chou KC.