NRPreTo: A Machine Learning-Based Nuclear Receptor and Subfamily Prediction Tool

Sita Sirisha Madugula, Suman Pandey, Shreya Amalapurapu, Serdar Bozdag

Research output: Contribution to journalArticlepeer-review

1 Scopus citations

Abstract

The nuclear receptor (NR) superfamily includes phylogenetically related ligand-activated proteins, which play a key role in various cellular activities. NR proteins are subdivided into seven subfamilies based on their function, mechanism, and nature of the interacting ligand. Developing robust tools to identify NR could give insights into their functional relationships and involvement in disease pathways. Existing NR prediction tools only use a few types of sequence-based features and are tested on relatively similar independent datasets; thus, they may suffer from overfitting when extended to new genera of sequences. To address this problem, we developed Nuclear Receptor Prediction Tool (NRPreTo), a two-level NR prediction tool with a unique training approach where in addition to the sequence-based features used by existing NR prediction tools, six additional feature groups depicting various physiochemical, structural, and evolutionary features of proteins were utilized. The first level of NRPreTo allows for the successful prediction of a query protein as NR or non-NR and further subclassifies the protein into one of the seven NR subfamilies in the second level. We developed Random Forest classifiers to test on benchmark datasets, as well as the entire human protein datasets from RefSeq and Human Protein Reference Database (HPRD). We observed that using additional feature groups improved the performance. We also observed that NRPreTo achieved high performance on the external datasets and predicted 59 novel NRs in the human proteome. The source code of NRPreTo is publicly available at https://github.com/bozdaglab/NRPreTo.

Original languageEnglish
Pages (from-to)20379-20388
Number of pages10
JournalACS Omega
Volume8
Issue number23
DOIs
StatePublished - Jun 13 2023
Externally publishedYes

Fingerprint

Dive into the research topics of 'NRPreTo: A Machine Learning-Based Nuclear Receptor and Subfamily Prediction Tool'. Together they form a unique fingerprint.

Cite this