Journal of chemical information and modeling
Dec 26, 2024
In recent years, the deep learning (DL) technique has rapidly developed and shown great success in scoring the protein-ligand binding affinities. The protein-ligand conformation optimization based on DL-derived scoring functions holds broad applicati...
Biochemical and biophysical research communications
Dec 24, 2024
Utilizing Artificial Intelligence (AI) in computational biology techniques could offer significant advantages in alleviating the growing workloads faced by structural biologists, especially with the emergence of big data. In this study, we employed D...
Protein-ligand interactions are the molecular basis of many important cellular activities, such as gene regulation, cell metabolism, and signal transduction. Protein-ligand binding affinity is a crucial metric of the strength of the interaction betwe...
Thermophilic proteins, mesophiles proteins and psychrophilic proteins have wide industrial applications, as enzymes with different optimal temperatures are often needed for different purposes. Convenient methods are needed to determine the optimal te...
Nuclear magnetic resonance (NMR) spectroscopy is an important technique for deriving the dynamics and interactions of macromolecules; however, characterizations of aromatic residues in proteins still pose a challenge. Here, we present a deep neural n...
Journal of chemical theory and computation
Dec 19, 2024
Helices are important secondary structural motifs within proteins and are pivotal in numerous physiological processes. While amino acids (AA) such as alanine and leucine are known to promote helix formation, proline and glycine disfavor it. Helical s...
Journal of chemical information and modeling
Dec 17, 2024
Large language models (LLMs) have transformed natural language processing, enabling advanced human-machine communication. Similarly, in computational biology, protein sequences are interpreted as natural language, facilitating the creation of protein...
Advanced science (Weinheim, Baden-Wurttemberg, Germany)
Dec 12, 2024
Proteins play an essential role in various biological and engineering processes. Large protein language models (PLMs) present excellent potential to reshape protein research by accelerating the determination of protein functions and the design of pro...
Binding affinity prediction has been considered as a fundamental task in drug discovery. Despite much effort to improve accuracy of binding affinity prediction, the prior work considered only macro-level features that can represent the characteristic...
Biomolecular condensates are membraneless organelles that can concentrate hundreds of different proteins in cells to operate essential biological functions. However, accurate identification of their components remains challenging and biased towards p...
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