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PUNCH: An Interactive Web Server for Predicting Intrinsically Disordered Regions in Protein Sequences

Year: 2025
Type: article
Abstract: • Fast IDR Prediction: PUNCH web server uses deep learning to detect IDRs accurately. • Lightweight Predictor: PUNCH2-Light leverages One-Hot and ProtTrans embeddings, avoiding slow MSA. • Broad Accessibility : Free web server with interactive visualisation and downloadable outputs. • Extensive Validation : Benchmarked on CAID2 with competitive accuracy and high-speed processing. • User-Centric Features : Adjustable thresholds, interactive plots, and comprehensive documentation for all users. PUNCH is a freely accessible web server designed for the rapid and accurate prediction of intrinsically disordered regions (IDRs) in protein sequences. Built on a high-performance computational framework, PUNCH web server which built on PUNCH2-Light predictor, combines speed with predictive accuracy, offering users a streamlined interface for generating predictions from sequence input. Validated against the CAID2 benchmarking datasets, PUNCH web server demonstrates competitive performance in detecting IDRs across diverse protein sequences. Notably, it excels in the Disorder_PDB dataset and provides reliable results for the Disorder_NOX dataset, addressing the challenges of predicting disordered regions with low sequence similarity. The server is available at https://alienlabs.ucd.ie/punch2/ , with extensive documentation and downloadable example datasets to support researchers in structural biology and bioinformatics.
DOI: 10.1016/j.jmb.2025.169018
Language: English
Open Access status: hybrid
Estimated APC paid: $4,730
OpenAlex ID: W4407776843
FWCI: 0.504
Cites: 12
Cited by: 2
Related to: 10