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Cold Spring Harbor perspectives in biology
Dec 1, 2023
Computing tools and machine learning models play an increasingly important role in biology and are now an essential part of discoveries in protein science. The growing energy needs of modern algorithms have raised concerns in the computational scienc...
Computer methods and programs in biomedicine
Nov 30, 2023
BACKGROUND AND OBJECTIVE: Protein-protein interaction (PPI) is a vital process in all living cells, controlling essential cell functions such as cell cycle regulation, signal transduction, and metabolic processes with broad applications that include ...
The journal of physical chemistry letters
Nov 30, 2023
Accurate prediction of binding free energy changes upon mutations is vital for optimizing drugs, designing proteins, understanding genetic diseases, and cost-effective virtual screening. While machine learning methods show promise in this domain, ach...
Proceedings of the National Academy of Sciences of the United States of America
Nov 30, 2023
There has been considerable progress in the development of computational methods for designing protein-protein interactions, but engineering high-affinity binders without extensive screening and maturation remains challenging. Here, we test a protein...
Molecules (Basel, Switzerland)
Nov 30, 2023
In recent years, the widespread application of artificial intelligence algorithms in protein structure, function prediction, and de novo protein design has significantly accelerated the process of intelligent protein design and led to many noteworthy...
BMC bioinformatics
Nov 28, 2023
Protein ubiquitination is a critical post-translational modification (PTMs) involved in numerous cellular processes. Identifying ubiquitination sites (Ubi-sites) on proteins offers valuable insights into their function and regulatory mechanisms. Due ...
Scientific reports
Nov 28, 2023
Protein-peptide interactions play a crucial role in various cellular processes and are implicated in abnormal cellular behaviors leading to diseases such as cancer. Therefore, understanding these interactions is vital for both functional genomics and...
Nature communications
Nov 28, 2023
Protein misfolding and aggregation play central roles in the pathogenesis of various neurodegenerative diseases (NDDs), including Huntington's disease, which is caused by a genetic mutation in exon 1 of the Huntingtin protein (Httex1). The fluorescen...
Science advances
Nov 22, 2023
Chemical shift assignment is vital for nuclear magnetic resonance (NMR)-based studies of protein structures, dynamics, and interactions, providing crucial atomic-level insight. However, obtaining chemical shift assignments is labor intensive and requ...
Journal of chemical information and modeling
Nov 20, 2023
Accurate in silico prediction of protein-ligand binding affinity is important in the early stages of drug discovery. Deep learning-based methods exist but have yet to overtake more conventional methods such as giga-docking largely due to their lack o...