Free energy and kinetic rate calculation via non-equilibrium molecular simulation: application to biomolecules
S Iida, K Tomoshi - Biophysical Reviews, 2022 - Springer
Non-equilibrium molecular dynamics (NEMD) simulation has been recognized as a powerful
tool for examining biomolecules and provides fruitful insights into not only non-equilibrium …
tool for examining biomolecules and provides fruitful insights into not only non-equilibrium …
No dance, no partner! A tale of receptor flexibility in docking and virtual screening
Modern drug design relies on a detailed understanding of the molecular recognition process
by which biological partners such as a protein and a drug interact and bind to each other …
by which biological partners such as a protein and a drug interact and bind to each other …
PathDetect-SOM: A neural network approach for the identification of pathways in ligand binding simulations
Understanding the process of ligand–protein recognition is important to unveil biological
mechanisms and to guide drug discovery and design. Enhanced-sampling molecular …
mechanisms and to guide drug discovery and design. Enhanced-sampling molecular …
Molecular Dynamics for the Optimal Design of Functionalized Nanodevices to Target Folate Receptors on Tumor Cells
Atomistic details on the mechanism of targeting activity by biomedical nanodevices of
specific receptors are still scarce in the literature, where mostly ligand/receptor pairs are …
specific receptors are still scarce in the literature, where mostly ligand/receptor pairs are …
Recognizing the binding pattern and dissociation pathways of the p300 Taz2-p53 TAD2 complex
The dynamic association and dissociation between proteins are the basis of cellular signal
transduction. This process becomes much more complicated if one or both interaction …
transduction. This process becomes much more complicated if one or both interaction …
Unlocking the Potential of Field Effect Transistor (FET) Biosensors: A Perspective on Methodological Advances in Computational and Molecular Biology
Abstract Field‐effect transistor (FET)‐based sensors are increasingly gaining relevance in
diagnostic, healthcare, and environmental monitoring applications. A FET operates by …
diagnostic, healthcare, and environmental monitoring applications. A FET operates by …
[HTML][HTML] Multimerization of HIF enhances transcription of target genes containing the hypoxia ancillary sequence
Transcriptional activity of the hypoxia inducible factor (HIF) relies on the formation of a
heterodimer composed of an oxygen-regulated α-subunit and a stably expressed β-subunit …
heterodimer composed of an oxygen-regulated α-subunit and a stably expressed β-subunit …
Metadynamics simulations for the investigation of drug loading on functionalized inorganic nanoparticles
Inorganic nanoparticles show promising properties that allow them to be efficiently used as
drug carriers. The main limitation in this type of application is currently the drug loading …
drug carriers. The main limitation in this type of application is currently the drug loading …
Mechanism of RGD-conjugated nanodevice binding to its target protein integrin α V β 3 by atomistic molecular dynamics and machine learning
Active targeting strategies have been proposed to enhance the selective uptake of
nanoparticles (NPs) by diseased cells, and recent experimental findings have proven the …
nanoparticles (NPs) by diseased cells, and recent experimental findings have proven the …
Insight into the initial stages of the folding process in onconase revealed by UNRES
The unfolded state of proteins presents many challenges to elucidate the structural basis for
biological function. This state is characterized by a large degree of structural heterogeneity …
biological function. This state is characterized by a large degree of structural heterogeneity …