Journal of chemical information and modeling
Jun 3, 2024
Raman spectroscopy is an important tool in the study of vibrational properties and composition of molecules, peptides, and even proteins. Raman spectra can be simulated based on the change of the electronic polarizability with vibrations, which can n...
Journal of molecular graphics & modelling
May 25, 2024
Elucidating unknown structures of proteins, such as metastable states, is critical in designing therapeutic agents. Protein structure exploration has been performed using advanced computational methods, especially molecular dynamics and Markov chain ...
Current opinion in structural biology
May 24, 2024
New high-performance computing architectures are becoming operative, in addition to exascale computers. Quantum computers (QC) solve optimization problems with unprecedented efficiency and speed, while neuromorphic hardware (NMH) simulates neural net...
Biomacromolecule structures are essential for drug development and biocatalysis. Quantum refinement (QR) methods, which employ reliable quantum mechanics (QM) methods in crystallographic refinement, showed promise in improving the structural quality ...
The phosphorylation of different sites produces a significant effect on the conformational dynamics of KRAS. Gaussian accelerated molecular dynamics (GaMD) simulations were combined with deep learning (DL) to explore the molecular mechanism of the ph...
Allostery is a fundamental mechanism driving biomolecular processes that holds significant therapeutic concern. Our study rigorously investigates how two distinct machine-learning algorithms uniquely classify two already close-to-active DFG-in states...
Current opinion in structural biology
May 13, 2024
Computational approaches can provide highly detailed insight into the molecular recognition processes that underlie drug binding, the assembly of protein complexes, and the regulation of biological functional processes. Classical simulation methods c...
Large language models have greatly enhanced our ability to understand biology and chemistry, yet robust methods for structure-based drug discovery, quantum chemistry and structural biology are still sparse. Precise biomolecule-ligand interaction data...
International journal of biological macromolecules
May 9, 2024
Shanxi aged vinegar microbiome encodes a wide variety of bacteriocins. The aim of this study was to mine, screen and characterize novel broad-spectrum bacteriocins from the large-scale microbiome data of Shanxi aged vinegar through machine learning, ...
This study aimed to identify potential BCL-2 small molecule inhibitors using deep neural networks (DNN) and random forest (RF), algorithms as well as molecular docking and molecular dynamics (MD) simulations to screen a library of small molecules. Th...