Perspective: Advances, challenges, and insight for predictive coarse-grained models

WG Noid - The Journal of Physical Chemistry B, 2023 - ACS Publications
By averaging over atomic details, coarse-grained (CG) models provide profound
computational and conceptual advantages for studying soft materials. In particular, bottom …

Computer simulations of deep eutectic solvents: Challenges, solutions, and perspectives

D Tolmachev, N Lukasheva, R Ramazanov… - International journal of …, 2022 - mdpi.com
Deep eutectic solvents (DESs) are one of the most rapidly evolving types of solvents,
appearing in a broad range of applications, such as nanotechnology, electrochemistry …

Extending the Martini 3 coarse-grained force field to carbohydrates

V Lutsyk, P Wolski, W Plazinski - Journal of Chemical Theory and …, 2022 - ACS Publications
Carbohydrates play an essential role in a large number of chemical and biochemical
processes. High structural diversity and conformational heterogeneity make it problematic to …

Application of molecular dynamics simulation in self-assembled cancer nanomedicine

X Xu, A Liu, S Liu, Y Ma, X Zhang, M Zhang… - Biomaterials …, 2023 - spj.science.org
Self-assembled nanomedicine holds great potential in cancer theragnostic. The structures
and dynamics of nanomedicine can be affected by a variety of non-covalent interactions, so …

[HTML][HTML] Integrating cellular electron microscopy with multimodal data to explore biology across space and time

CL McCafferty, S Klumpe, RE Amaro, W Kukulski… - Cell, 2024 - cell.com
Biology spans a continuum of length and time scales. Individual experimental methods only
glimpse discrete pieces of this spectrum but can be combined to construct a more holistic …

Epicatechin is a promising novel inhibitor of SARS-CoV-2 entry by disrupting interactions between angiotensin-converting enzyme type 2 and the viral receptor …

MBS Al-Shuhaib, HO Hashim… - Computers in Biology and …, 2022 - Elsevier
Abstract Angiotensin-converting enzyme 2 (ACE2) is the first target of SARS-CoV-2 and a
key functional host receptor through which this virus hooks into and infects human cells. The …

[HTML][HTML] Utilizing Molecular Dynamics Simulations, Machine Learning, Cryo-EM, and NMR Spectroscopy to Predict and Validate Protein Dynamics

A Son, W Kim, J Park, W Lee, Y Lee, S Choi… - International Journal of …, 2024 - mdpi.com
Protein dynamics play a crucial role in biological function, encompassing motions ranging
from atomic vibrations to large-scale conformational changes. Recent advancements in …

Protein function analysis through machine learning

C Avery, J Patterson, T Grear, T Frater, DJ Jacobs - Biomolecules, 2022 - mdpi.com
Machine learning (ML) has been an important arsenal in computational biology used to
elucidate protein function for decades. With the recent burgeoning of novel ML methods and …

Exploring Free Energies of Specific Protein Conformations Using the Martini Force Field

W Plazinski, V Lutsyk, A Plazinska - Journal of Chemical Theory …, 2024 - ACS Publications
Coarse-grained (CG) level molecular dynamics simulations are routinely used to study
various biomolecular processes. The Martini force field is currently the most widely adopted …

Computational biophysics meets cryo‐EM revolution in the search for the functional dynamics of biomolecular systems

MGS Costa, M Gur, JM Krieger… - Wiley Interdisciplinary …, 2024 - Wiley Online Library
There is a variety of experimental and computational techniques available to explore protein
dynamics, each presenting advantages and limitations. One promising experimental …