Year: 2025
Type: article
Abstract: Background: Intrinsically disordered proteins (IDPs) are proteins that contain intrinsically disordered regions (IDRs), which lack stable three-dimensional structures under physiological conditions. These regions are known to play crucial roles in many biological processes. While IDRs can be predicted from their amino acid sequences, and several accurate IDR prediction programs have been developed, such programs often require substantial computational resources, including long execution times, large databases for homology searches, and advanced computer architectures. Since DNA sequence data continues to grow rapidly, particularly at a genomic scale, there is an increasing need for fast and accurate IDR prediction programs that demand fewer computational resources. Methods: In this study, we developed DARUMA (Disorder order clAssifier by Rapid and User-friendly MAchine), an IDR prediction program designed for speed and ease of use. DARUMA uses a one-dimensional convolutional neural network (1D-CNN) that processes the physicochemical properties of amino acid residues instead of relying on sequence profiles. DARUMA employs a simple neural network that predicts IDRs using the output of 1D-CNN as input features. To ensure easy installation on users' systems, DARUMA was written entirely in Python using standard and NumPy libraries. Results: DARUMA achieves fast performance by avoiding iterative homology searches while delivering accuracy comparable to the latest predictors that use sequence profiles. In addition to the advantage of execution time, DARUMA requires no additional homology search programs and operates using standard Python libraries, making it easy to install and run on users' own environments without the need for specialized computational resources. DARUMA is available at https://antepontem.org/daruma/, which also provides the stand-alone distribution.
Source: PeerJ Computer Science
Authors: Itsuki Shimizu, Takuya Ida, Yuhei Ozawa, Satoshi Fukuchi, Hiroto Anbo
Institution: Maebashi Institute of Technology
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: gold
Estimated APC paid: $1,395
OpenAlex ID: W4416197264