:: DESCRIPTION
SpectralNET is a tool to analyze networks of interactions, such as chemical-genetic networks
::DEVELOPER
The Broad Institute, Cambridge, MA
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
BMC Bioinformatics. 2005 Oct 19;6:260.
SpectralNET–an application for spectral graph analysis and visualization.
Forman JJ, Clemons PA, Schreiber SL, Haggarty SJ.
:: DESCRIPTION
Given a set of protein sequences (in fasta format), InterPreTS will use BLAST to find homologues of known structure for all pairs (i.e. templates that can model each pair of sequences based on homology) and then evaluate the suitability of those templates for modelling the interaction
::DEVELOPER
the Cell Networks Protein Evolution group based at the University of Heidelberg.
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Aloy P, Russell RB.
InterPreTS: protein interaction prediction through tertiary structure.
Bioinformatics. 2003 Jan;19(1):161-2.
:: 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
:: 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.
:: DESCRIPTION
RIscoper (RNA Interactome Scoper) represents the first tool for full-scale RNA interactome scanning and was developed for extracting RRIs from the literature based on the N-gram model.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Zhang Y, Liu T, Chen L, Yang J, Yin J, Zhang Y, Yun Z, Xu H, Ning L, Guo F, Jiang Y, Lin H, Wang D, Huang Y, Huang J.
RIscoper: a tool for RNA-RNA interaction extraction from the literature.
Bioinformatics. 2019 Sep 1;35(17):3199-3202. doi: 10.1093/bioinformatics/btz044. PMID: 30668649.
:: DESCRIPTION
DPPI uses a convolutional neural network to predict PPI interactions by using only the protein sequences.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Hashemifar S, Neyshabur B, Khan AA, Xu J.
Predicting protein-protein interactions through sequence-based deep learning.
Bioinformatics. 2018 Sep 1;34(17):i802-i810. doi: 10.1093/bioinformatics/bty573. PMID: 30423091; PMCID: PMC6129267.
:: DESCRIPTION
NIpredict is a method to predict nuclear import activity based on characterization of NLS-import receptor interaction using molecular interaction energy components (MIECs).
::DEVELOPER
Machine Learning and Evolution Laboratory (MLEG)
:: SCREENSHOTS
n/a
:: REQUIREMENTS
NO
:: MORE INFORMATION
Citation:
Proteins. 2014 Oct;82(10):2783-96. doi: 10.1002/prot.24642. Epub 2014 Jul 31.
Computational identification of post-translational modification-based nuclear import regulations by characterizing nuclear localization signal-import receptor interaction.
Lin JR1, Liu Z, Hu J.
:: DESCRIPTION
power GWAS interaction is the code for approximate power calculations for identification of gene x gene and gene x environment interactions in genomewide association studies using a two-stage analysis.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
C. Kooperberg and M. LeBlanc (2008).
Increasing the power of identifying gene x gene interactions in genome-wide association studies
Genetic Epidemiology, 32, 255-263.
:: DESCRIPTION
Cancerin is a tool to infer genome-wide cancer-associated ceRNA interaction network in cancer.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Do D, Bozdag S.
Cancerin: A computational pipeline to infer cancer-associated ceRNA interaction networks.
PLoS Comput Biol. 2018 Jul 16;14(7):e1006318. doi: 10.1371/journal.pcbi.1006318. PMID: 30011266; PMCID: PMC6072113.
:: DESCRIPTION
PathwaysWeb provides publicly available information on genes, biological pathways, Gene Ontology terms, gene gene interaction networks with interaction directionality, and links to related PubMed documents.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
PathwaysWeb: A Gene Pathways API with Directional Interactions, Expanded Gene Ontology, and Versioning.
Melott JM, Weinstein JN, Broom BM.
Bioinformatics. 2015 Sep 23. pii: btv554.
:: 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
:: DOWNLOAD
:: 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.