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Evaluation of Machine Learning/Molecular Mechanics End-State Corrections with Mechanical Embedding to Calculate Relative Protein-Ligand Binding Free Energies.
J Chem Theory Comput
January 2025
Exscientia, Schrödinger Building, Oxford Science Park, Oxford OX4 4GE, U.K.
The development of machine-learning (ML) potentials offers significant accuracy improvements compared to molecular mechanics (MM) because of the inclusion of quantum-mechanical effects in molecular interactions. However, ML simulations are several times more computationally demanding than MM simulations, so there is a trade-off between speed and accuracy. One possible compromise are hybrid machine learning/molecular mechanics (ML/MM) approaches with mechanical embedding that treat the intramolecular interactions of the ligand at the ML level and the protein-ligand interactions at the MM level.
View Article and Find Full Text PDFThe gap between surgeon goal and achieved sagittal alignment in adult cervical spine deformity surgery.
J Neurosurg Spine
January 2025
6Presbyterian St. Lukes Medical Center, Denver, Colorado.
Objective: Malalignment following cervical spine deformity (CSD) surgery can negatively impact outcomes and increase complications. Despite the growing ability to plan alignment, it remains unclear whether preoperative goals are achieved with surgery. The objective of this study was to assess how good surgeons are at achieving their preoperative goal alignment following CSD surgery.
View Article and Find Full Text PDFFull-Dimensional Neural Network Potential Energy Surface for the Photodissociation Dynamics of HNCS in the S band.
J Phys Chem A
January 2025
Institute of Modern Physics, Shaanxi Key Laboratory for Theoretical Physics Frontiers, Northwest University, Xi'an, Shaanxi 710127, China.
The full-dimensional potential energy surface (PES) for the photodissociation of HNCS in the S(″) electronic state has been built up by the neural network method based on more than 48,000 points, which were calculated at the multireference configuration interaction level with Davidson correction using the augmented correlation consistent polarized valence triple-ζ basis set. It was found that two minima, namely, and isomers of HNCS, and seven stationary points exist on the S PES for the three dissociation pathways: HNCS(S) → H + NCS/HNC + S(D)/HN(Δ) + CS(Σ). The dissociation energies of two lowest product channels H + NCS and HNC + S(D) calculated on the PES are in good agreement with experimental results, validating the high accuracy of the PES.
View Article and Find Full Text PDFBasic Science and Pathogenesis.
Alzheimers Dement
December 2024
David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.
Background: Progressive supranuclear palsy (PSP) is a neurodegenerative disorder involving pathological deposition of tau that includes glial inclusions and specific regional vulnerability patterns. Therapeutic developments are hampered by incomplete understanding of disease mechanisms. Few studies have examined its cell type-specific effects.
View Article and Find Full Text PDFDescription of changes in chemical bonding along the pathways of chemical reactions by deformation of the molecular electrostatic potential.
J Mol Model
January 2025
Department of Theoretical Chemistry, Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387, Krakow, Poland.
Context: The analysis of the changes in the electronic structure along intrinsic reaction coordinate (IRC) paths for model reactions: (i) ethylene + butadiene cycloaddition, (ii) prototype SN2 reaction Cl + CH3Cl, (iii) HCN/CNH isomerization assisted by water, (iv) CO + HF → C(O)HF was performed, in terms of changes in the deformation density (Δr) and the deformation of MEP (ΔMEP). The main goal was to further examine the utility of the ΔMEP as a descriptor of chemical bonding, and to compare the pictures resulting from Δr and ΔMEP. Both approaches clearly show that the main changes in the electronic structure occur in the TS region.
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