Journal of biomolecular structure & dynamics
Jul 24, 2023
Flavonoids, especially their inhibitory effect on DPP-IV activity, have been widely recognized for their antidiabetic effects. However, the variety of natural flavonoid derivatives is very rich, and even subtle structural differences can lead to seve...
PD-L1 is a key immunotarget involved in binding to its receptor PD-1. PD-L1/PD-1 interface blocking using antibodies (or small molecules) is the central area of interest for tumor suppression in various cancers. Blocking the PD-L1/PD-1 pathway in the...
CONTEXT: Staphylococcus aureus is a highly pathogenic organism that is the most common cause of postoperative complications as well as severe infections like bacteremia and infective endocarditis. By mediating the formation of biofilms and the expres...
Parkinson's disease is characterized by a multifactorial nature that is linked to different pathways. Among them, the abnormal deposition and accumulation of α-synuclein fibrils is considered a neuropathological hallmark of Parkinson's disease. Sever...
International journal of molecular sciences
Jul 17, 2023
During the outbreak of COVID-19, many SARS-CoV-2 variants presented key amino acid mutations that influenced their binding abilities with angiotensin-converting enzyme 2 (hACE2) and neutralizing antibodies. For the B.1.617 lineage, there had been fea...
Journal of biomolecular structure & dynamics
Jul 14, 2023
De novo generation of molecules with the necessary features offers a promising opportunity for artificial intelligence, such as deep generative approaches. However, creating novel compounds having biological activities toward two distinct targets con...
In the last decade, molecular dynamics (MD) simulations have become an essential tool to investigate the molecular properties of membrane trafficking processes, often in conjunction with experimental approaches. The combination of MD simulations with...
Journal of biomolecular structure & dynamics
Jun 20, 2023
Chronic disease patients (cancer, arthritis, cardiovascular diseases) undergo long-term systemic drug treatment. Membrane transporters in ocular barriers could falsely recognize these drugs and allow their trafficking into the eye from systemic circu...
Machine learning force fields (MLFFs) are gradually evolving towards enabling molecular dynamics simulations of molecules and materials with ab initio accuracy but at a small fraction of the computational cost. However, several challenges remain to b...
Journal of chemical information and modeling
Jun 12, 2023
Molecular dynamics simulation is an indispensable tool for understanding the collective behavior of atoms and molecules and the phases they form. Statistical mechanics provides accurate routes for predicting macroscopic properties as time-averages ov...
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