Intrinsically disordered proteins (IDPs) differ from folded proteins in that they are dynamic, lack a stable three-dimensional conformation, and have low sequence similarity between similar proteins.
The conformational heterogeneity of IDPs - while beneficial for their diverse functions - limits the use of traditional experimental tools to determine their conformation.
The experimental difficulty, along with low sequence similarity, results in data scarcity, and makes it difficult to classify/detect IDPs that are similar or dissimilar, a task relevant to understand biology and evolution.
We address this challenge using Multi-task ProtBERT (MT-ProtBERT), a multi-task extension of ProtBERT tailored for low-data regimes.
MT-ProtBERT integrates Dynamic Window Masking, a Multi-Scale 1D Convolutional classifier (MS-Conv1D), and auxiliary objectives that jointly optimize masked language modeling and biochemistry-informed tasks.
We evaluate this framework on two tasks under limited data: (i) phosphorylation site prediction (S/T/Y) in short sequences and small datasets, and (ii) protein compaction prediction on two small datasets (684 and 530 sequences), including sequences comparable in length to typical disordered regions.
MT-ProtBERT consistently outperforms PARROT, an RNN-based IDP-specific model, across all tasks.
These results demonstrate that combining self-supervised and biochemistry-informed tasks, and multi-scale learning enables robust modeling of unstructured proteins under data scarcity.