On the emergence of machine-learning methods in bottom-up coarse-graining
PG Sahrmann, GA Voth - Current Opinion in Structural Biology, 2025 - Elsevier
Machine-learning methods have gained significant attention in the computational chemistry
community as a viable approach to molecular modeling and analysis. Recent successes in …
community as a viable approach to molecular modeling and analysis. Recent successes in …
Megamolecule Self-Assembly Networks: A Combined Computational and Experimental Design Strategy
This work describes the use of computational strategies to design megamolecule building
blocks for the self-assembly of lattice networks. The megamolecules are prepared by …
blocks for the self-assembly of lattice networks. The megamolecules are prepared by …
QM/CG-MM: Systematic Embedding of Quantum Mechanical Systems in a Coarse-Grained Environment with Accurate Electrostatics
Quantum Mechanics/Molecular Mechanics (QM/MM) can describe chemical reactions in
molecular dynamics (MD) simulations at a much lower cost than ab initio MD. Still, it is …
molecular dynamics (MD) simulations at a much lower cost than ab initio MD. Still, it is …
Analysis of mapping atomic models to coarse-grained resolution
KM Kidder, WG Noid - The Journal of Chemical Physics, 2024 - pubs.aip.org
Low-resolution coarse-grained (CG) models provide significant computational and
conceptual advantages for simulating soft materials. However, the properties of CG models …
conceptual advantages for simulating soft materials. However, the properties of CG models …
Data-Driven Equation-Free Dynamics Applied to Many-Protein Complexes: The Microtubule Tip Relaxation
Microtubules (MTs) constitute the largest components of the eukaryotic cytoskeleton and
play crucial roles in various cellular processes, including mitosis and intracellular transport …
play crucial roles in various cellular processes, including mitosis and intracellular transport …
Stabilization Mechanism of Initiator Transfer RNA in the Small Ribosomal Subunit from Coarse-Grained Molecular Simulations
Proteins play a variety of roles in biological phenomena in cells. Proteins are synthesized by
the ribosome, which is a large molecular complex composed of proteins and nucleic acids …
the ribosome, which is a large molecular complex composed of proteins and nucleic acids …
Dynamic framework for large-scale modeling of membranes and peripheral proteins.
M Sadeghi, D Rosenberger - Methods in Enzymology, 2024 - europepmc.org
In this chapter, we present a novel computational framework to study the dynamic behavior
of extensive membrane systems, potentially in interaction with peripheral proteins, as an …
of extensive membrane systems, potentially in interaction with peripheral proteins, as an …