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 …

No dance, no partner! A tale of receptor flexibility in docking and virtual screening

A Basciu, L Callea, S Motta, AMJJ Bonvin… - Annual Reports in …, 2022 - Elsevier
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 …

PathDetect-SOM: A neural network approach for the identification of pathways in ligand binding simulations

S Motta, L Callea, L Bonati… - Journal of Chemical Theory …, 2022 - ACS Publications
Understanding the process of ligand–protein recognition is important to unveil biological
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

E Donadoni, G Frigerio, P Siani, S Motta… - ACS Biomaterials …, 2023 - ACS Publications
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 …

Recognizing the binding pattern and dissociation pathways of the p300 Taz2-p53 TAD2 complex

T Li, S Motta, AO Stevens, S Song, E Hendrix… - JACS Au, 2022 - ACS Publications
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 …

Unlocking the Potential of Field Effect Transistor (FET) Biosensors: A Perspective on Methodological Advances in Computational and Molecular Biology

J Rexha, N Perta, A Roscioni, S Motta… - Advanced Sensor …, 2023 - Wiley Online Library
Abstract Field‐effect transistor (FET)‐based sensors are increasingly gaining relevance in
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

T Rosell-Garcia, S Rivas-Muñoz, K Kin… - … et Biophysica Acta (BBA …, 2023 - Elsevier
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 …

Metadynamics simulations for the investigation of drug loading on functionalized inorganic nanoparticles

S Motta, P Siani, E Donadoni, G Frigerio, L Bonati… - Nanoscale, 2023 - pubs.rsc.org
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 …

Mechanism of RGD-conjugated nanodevice binding to its target protein integrin α V β 3 by atomistic molecular dynamics and machine learning

G Frigerio, E Donadoni, P Siani, J Vertemara, S Motta… - Nanoscale, 2024 - pubs.rsc.org
Active targeting strategies have been proposed to enhance the selective uptake of
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

E Hendrix, S Motta, RF Gahl, Y He - The Journal of Physical …, 2022 - ACS Publications
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 …