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 …
computational and conceptual advantages for studying soft materials. In particular, bottom …
Molecular dynamics simulations of large macromolecular complexes
Connecting dynamics to structural data from diverse experimental sources, molecular
dynamics simulations permit the exploration of biological phenomena in unparalleled detail …
dynamics simulations permit the exploration of biological phenomena in unparalleled detail …
Random heteropolymers preserve protein function in foreign environments
The successful incorporation of active proteins into synthetic polymers could lead to a new
class of materials with functions found only in living systems. However, proteins rarely …
class of materials with functions found only in living systems. However, proteins rarely …
Chemically specific coarse‐graining of polymers: Methods and prospects
S Dhamankar, MA Webb - Journal of Polymer Science, 2021 - Wiley Online Library
Coarse‐grained (CG) modeling is an invaluable tool for the study of polymers and other soft
matter systems due to the span of spatiotemporal scales that typify their physics and …
matter systems due to the span of spatiotemporal scales that typify their physics and …
Perspective: Coarse-grained models for biomolecular systems
WG Noid - The Journal of chemical physics, 2013 - pubs.aip.org
By focusing on essential features, while averaging over less important details, coarse-
grained (CG) models provide significant computational and conceptual advantages with …
grained (CG) models provide significant computational and conceptual advantages with …
Deep geometric representations for modeling effects of mutations on protein-protein binding affinity
Modeling the impact of amino acid mutations on protein-protein interaction plays a crucial
role in protein engineering and drug design. In this study, we develop GeoPPI, a novel …
role in protein engineering and drug design. In this study, we develop GeoPPI, a novel …
Coarse-graining methods for computational biology
MG Saunders, GA Voth - Annual review of biophysics, 2013 - annualreviews.org
Connecting the molecular world to biology requires understanding how molecular-scale
dynamics propagate upward in scale to define the function of biological structures. To …
dynamics propagate upward in scale to define the function of biological structures. To …
[HTML][HTML] Spike proteins of SARS-CoV and SARS-CoV-2 utilize different mechanisms to bind with human ACE2
The ongoing outbreak of COVID-19 has been a serious threat to human health worldwide.
The virus SARS-CoV-2 initiates its infection to the human body via the interaction of its spike …
The virus SARS-CoV-2 initiates its infection to the human body via the interaction of its spike …
Combining an elastic network with a coarse-grained molecular force field: structure, dynamics, and intermolecular recognition
X Periole, M Cavalli, SJ Marrink… - Journal of chemical …, 2009 - ACS Publications
Structure-based and physics-based coarse-grained molecular force fields have become
attractive approaches to gain mechanistic insight into the function of large biomolecular …
attractive approaches to gain mechanistic insight into the function of large biomolecular …
Flexible fitting of atomic structures into electron microscopy maps using molecular dynamics
A novel method to flexibly fit atomic structures into electron microscopy (EM) maps using
molecular dynamics simulations is presented. The simulations incorporate the EM data as …
molecular dynamics simulations is presented. The simulations incorporate the EM data as …