Nature methods
Dec 8, 2023
Three-dimensional structure modeling from maps is an indispensable step for studying proteins and their complexes with cryogenic electron microscopy. Although the resolution of determined cryogenic electron microscopy maps has generally improved, the...
Journal of proteome research
Dec 6, 2023
O-linked β--acetylglucosamine (O-GlcNAc) is a post-translational modification (i.e., O-GlcNAcylation) on serine/threonine residues of proteins, regulating a plethora of physiological and pathological events. As a dynamic process, O-GlcNAc functions i...
Computers in biology and medicine
Dec 5, 2023
Protein contact map prediction is a critical and vital step in protein structure prediction, and its accuracy is highly contingent upon the feature representations of protein sequence information and the efficacy of deep learning models. In this pape...
Journal of chromatography. B, Analytical technologies in the biomedical and life sciences
Dec 1, 2023
Universal health care is attracting increased attention nowadays, because of the large increase in population all over the world, and a similar increase in life expectancy, leading to an increase in the incidence of non-communicable (various cancers,...
Proceedings of the National Academy of Sciences of the United States of America
Dec 1, 2023
Enhancing protein thermal stability is important for biomedical and industrial applications as well as in the research laboratory. Here, we describe a simple machine-learning method which identifies amino acid substitutions that contribute to thermal...
Communications biology
Dec 1, 2023
Accurately capturing domain-domain interactions is key to understanding protein function and designing structure-based drugs. Although AlphaFold2 has made a breakthrough on single domain, it should be noted that the structure modeling for multi-domai...
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...