:: DESCRIPTION
HubPredictor is the R function to run Bayesian Additive Regression Trees (BART) model for predicting chromatin interaction hubs using histone marks information.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: 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
:: 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
:: 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.
:: 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
:: DOWNLOAD
:: 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.
:: 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
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: 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
:: 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
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: 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.
:: DESCRIPTION
POW is a website that allows users to predict PDZ domain-peptide interactions for human, mouse, worm and fly PDZ domains.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: 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.
:: DESCRIPTION
DoMo-Pred is a Domain-Motif Mediated Interaction Prediction command line tool
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Predicting physiologically relevant SH3 domain mediated protein-protein interactions in yeast.
Jain S, Bader GD.
Bioinformatics. 2016 Feb 9. pii: btw045.
:: DESCRIPTION
ExRAT is a program for testing association between a disease and SNP pairs with interaction.
::DEVELOPER
Laboratory for Medical Science Mathematics
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: 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
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: 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.
:: 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
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: 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.