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Optical camera communication (OCC) provides license-free communication channels without radio waves. The rolling shutter mechanism is expected to enhance the capacity of wireless links in OCC. However, signal erasure occurs due to waiting times between frames in consecutive signal transmission.
View Article and Find Full Text PDFStandard Binding Free-Energy Calculations: How Far Are We from Automation?
J Phys Chem B
December 2023
State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Sciences, Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin 300071, China.
Recent success stories suggest that in silico protein-ligand binding free-energy calculations are approaching chemical accuracy. However, their widespread application remains limited by the extensive human intervention required, posing challenges for the neophyte. As such, it is critical to develop automated workflows for estimating protein-ligand binding affinities with minimum personal involvement.
View Article and Find Full Text PDFAchieving Accurate Standard Protein-Protein Binding Free Energy Calculations through the Geometrical Route and Ergodic Sampling.
J Chem Inf Model
April 2023
Research Center for Analytical Sciences, Frontiers Science Center for New Organic Matter, College of Chemistry, Tianjin Key Laboratory of Biosensing and Molecular Recognition, State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300071, China.
A new strategy for the prediction of binding free energies of protein-protein complexes is reported in the present article. By combining an ergodic-sampling algorithm with the so-called "geometrical route", which introduces a series of geometrical restraints as a preamble to the physical separation of the two partners, we achieve accurate binding free energy calculations for medium-sized protein-protein complexes within the microsecond timescale. The ergodic-sampling algorithm, namely, Gaussian-accelerated molecular dynamics (GaMD), implicitly helps explore the conformational change of the two binding partners as they associate reversibly by raising the energy wells.
View Article and Find Full Text PDFThe preamble to the free radical biology and medicine virtual special issue on "Targeting genetic biosensors to intracellular signaling pathways".
Free Radic Biol Med
July 2022
Molecular Biology and Biochemistry, Gottfried Schatz Research Center, Medical University of Graz, 8010, Graz, Austria; BioTechMed Graz, Mozartgasse 12/II, 8010, Graz, Austria. Electronic address:
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