HubPredictor is the R function to run Bayesian Additive Regression Trees (BART) model for predicting chromatin interaction hubs using histone marks information.
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.
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.
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
DT-Hybrid is an R package that implements the homonymous algorithm for the prediction of interactions between small-molecules (i.e. Drug-Target Interactions).
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.
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