IEEE/ACM transactions on computational biology and bioinformatics
Dec 8, 2022
Protein-DNA interactions play an important role in diverse biological processes. Accurately identifying protein-DNA binding residues is a critical but challenging task for protein function annotations and drug design. Although wet-lab experimental me...
IEEE/ACM transactions on computational biology and bioinformatics
Dec 8, 2022
Essential proteins are considered the foundation of life as they are indispensable for the survival of living organisms. Computational methods for essential protein discovery provide a fast way to identify essential proteins. But most of them heavily...
IEEE/ACM transactions on computational biology and bioinformatics
Dec 8, 2022
BACKGROUND: Much of the recent success in protein structure prediction has been a result of accurate protein contact prediction-a binary classification problem. Dozens of methods, built from various types of machine learning and deep learning algorit...
IEEE/ACM transactions on computational biology and bioinformatics
Dec 8, 2022
Pretrained representations have recently gained attention in various machine learning applications. Nonetheless, the high computational costs associated with training these models have motivated alternative approaches for representation learning. Her...
Ubiquitination is an important post-translational modification of proteins that regulates many cellular activities. Traditional experimental methods for identification are costly and time-consuming, so many researchers have proposed computational met...
The protein secondary structure (SS) prediction plays an important role in the characterization of general protein structure and function. In recent years, a new generation of algorithms for SS prediction based on embeddings from protein language mod...
BACKGROUND: Protein-protein interactions are widespread in biological systems and play an important role in cell biology. Since traditional laboratory-based methods have some drawbacks, such as time-consuming, money-consuming, etc., a large number of...
International journal of molecular sciences
Nov 29, 2022
The body of scientific literature continues to grow annually. Over 1.5 million abstracts of biomedical publications were added to the PubMed database in 2021. Therefore, developing cognitive systems that provide a specialized search for information i...
Artificial intelligence-based protein structure prediction approaches have had a transformative effect on biomolecular sciences. The predicted protein models in the AlphaFold protein structure database, however, all lack coordinates for small molecul...
The prediction of mechanical and dynamical properties of proteins is an important frontier, especially given the greater availability of proteins structures. Here we report a series of models that provide end-to-end predictions of nanodynamical prope...