NetControl4BioMed: a web-based platform for controllability analysis of protein–protein interaction networks

Abstract

Abstract Motivation There is an increasing amount of data coming from genome-wide studies identifying disease-specific survivability-essential proteins and host factors critical to a cell becoming infected. Targeting such proteins has a strong potential for targeted, precision therapies. Typically however, too few of them are drug targetable. An alternative approach is to influence them through drug targetable proteins upstream of them. Structural target network controllability is a suitable solution to this problem. It aims to discover suitable source nodes (e.g. drug targetable proteins) in a directed interaction network that can control (through a suitable set of input functions) a desired set of targets. Results We introduce NetControl4BioMed, a free open-source web-based application that allows users to generate or upload directed protein–protein interaction networks and to perform target structural network controllability analyses on them. The analyses can be customized to focus the search on drug targetable source nodes, thus providing drug therapeutic suggestions. The application integrates protein data from HGNC, Ensemble, UniProt, NCBI and InnateDB, directed interaction data from InnateDB, Omnipath and SIGNOR, cell-line data from COLT and DepMap, and drug–target data from DrugBank. Availabilityand implementation The application and data are available online at https://netcontrol.combio.org/. The source code is available at https://github.com/Vilksar/NetControl4BioMed under an MIT license.