STITCH 5.0 – Search Tool for Interactions of Chemicals and proteins

STITCH 5.0

:: DESCRIPTION

STITCH (search tool for interactions of chemicals)  is a resource to explore known and predicted interactions of chemicals and proteins.Chemicals are linked to other chemicals and proteins by evidence derived from experiments, databases and the literature.

::DEVELOPER

Bork Group

:: SCREENSHOTS

:: REQUIREMENTS

  • Web Browser / Linux

:: DOWNLOAD

 STITCH

:: MORE INFORMATION

Citation

STITCH 5: augmenting protein-chemical interaction networks with tissue and affinity data.
Szklarczyk D, Santos A, von Mering C, Jensen LJ, Bork P, Kuhn M.
Nucleic Acids Res. 2015 Nov 20. pii: gkv1277.

Nucleic Acids Res. 2014 Jan;42(Database issue):D401-7. doi: 10.1093/nar/gkt1207. Epub 2013 Nov 28.
STITCH 4: integration of protein-chemical interactions with user data.
Kuhn M1, Szklarczyk D, Pletscher-Frankild S, Blicher TH, von Mering C, Jensen LJ, Bork P.

STITCH: interaction networks of chemicals and proteins.
Kuhn M, von Mering C, Campillos M, Jensen LJ, Bork P
Nucleic Acids Res. 2008 Jan 15; 36: D684-8. Epub 2007 Dec 15; PubMed: 18084021.

Ar_NHPred – Prediction of Aromatic Backbone NH Interaction in Proteins

Ar_NHPred

:: DESCRIPTION

Ar_NHPred is a web server for predicting the aromatic backbone NH interaction in a given amino acid sequence where the pi ring of aromatic residues interact with the backbone NH groups. The method is based on the neural network training on PSI-BLAST generated position specific matrices and PSIPRED predicted secondary structure

::DEVELOPER

Dr. G P S Raghava

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Kaur, H. and Raghava, G. P. S. (2004)
Role of evolutionary information in prediction of aromatic-backbone NH interactions in proteins.
FEBS Letters 564:47-57.

Pprint – Prediction of Protein RNA- Interaction

Pprint

:: DESCRIPTION

Pprint is a web-server for predicting RNA-binding residues of a protein.

::DEVELOPER

Pprint team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Proteins. 2008 Apr;71(1):189-94.
Prediction of RNA binding sites in a protein using SVM and PSSM profile.
Kumar M1, Gromiha MM, Raghava GP.

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.

BkTree 20160124 – Prediction of RNA Nucleotide Interactions with Backbone k-Tree Model

BkTree 20160124

:: DESCRIPTION

BkTree is an utility capable of predicting all familites of RNA nucleotide interactions, including base-base, base-phosphate, base-ribose, and base-stacking interactions, from the input query sequence (along with predicted or known canonical Watson-Crick base pairs).

::DEVELOPER

The RNA-Informatics Research Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 BkTree

:: MORE INFORMATION

Citation

Accurate Prediction of RNA Nucleotide Interactions with Backbone k-Tree Model.
Ding L, Xue X, LaMarca S, Mohebbi M, Samad A, Malmberg RL, Cai L.
Bioinformatics. 2015 Apr 16. pii: btv210.

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.

EPI-Peptide Designer – Designing Specific Peptide Ligand Libraries based on Epitope-Paratope Interactions

EPI-Peptide Designer

:: DESCRIPTION

EPI-Peptide Designer tool predicted paratope residues for an epitope of interest to generate targeted peptide ligand libraries.

::DEVELOPER

the Protein Computational Biology group.

:: SCREENSHOTS

EPI-Peptide

:: REQUIREMENTS

  • Linux/ Windows
  • Java

:: DOWNLOAD

 EPI-Peptide Designer

:: MORE INFORMATION

Citation

EPI-Peptide Designer : a tool for designing specific peptide ligand libraries based on Epitope-Paratope Interactions.
Viart B, Gonzalez E, Dias-Lopes C, Oliveira CF, Nguyen C, Neshich G, Chávez-Olórtegui C, Molina F, Felicori L.
Bioinformatics. 2016 Jan 18. pii: btw014.

multiMiR 1.0.1 – Integration of microRNA-target Interactions along with their Disease and Drug Associations

multiMiR 1.0.1

:: DESCRIPTION

The R package multiMiR is a comprehensive collection of predicted and validated miRNA-target interactions and their associations with diseases and drugs.

::DEVELOPER

Yuanbin Ru at Windber Research Institute & Katerina Kechris at the University of Colorado Denver.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux
  • R

:: DOWNLOAD

 multiMiR

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2014;42(17):e133. doi: 10.1093/nar/gku631. Epub 2014 Jul 24.
The multiMiR R package and database: integration of microRNA-target interactions along with their disease and drug associations.
Ru Y, Kechris KJ, Tabakoff B, Hoffman P, Radcliffe RA, Bowler R, Mahaffey S, Rossi S, Calin GA, Bemis L, Theodorescu D.

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

JCI BioInfo 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