CPIExtract: A software package to collect and harmonize small molecule and protein interactions

Abstract

Summary: The binding interactions between small molecules and proteins are the basis of cellular functions. Yet, experimental data available regarding compound-protein interaction are not harmonized into a single entity but rather scattered across multiple institutions, each maintaining databases with different formats. Extracting information from these multiple sources remains challenging due to data heterogeneity. Here, we present CPIExtract (Compound-Protein Interaction Extract), a tool to interactively extract experimental binding interaction data from multiple databases, perform filtering, and harmonize the resulting information, thus providing a gain of compound-protein interaction data. When compared to a single source, DrugBank, we show that it can collect more than ten times the number of annotations. The end-user can apply custom filtering to the aggregated output data and save it in any generic tabular file suitable for further downstream tasks such as network medicine analyses for drug repurposing and cross-validation of deep learning models. Availability: CPIExtract is an open-source Python package under an MIT license. CPIExtract can be installed from https://pypi.org/project/cpiextract and downloaded from https://github.com/menicgiulia/CPIExtract. The package can run on any standard desktop computer or computing cluster.