Two decades of Martini: Better beads, broader scope
The Martini model, a coarse‐grained force field for molecular dynamics simulations, has
been around for nearly two decades. Originally developed for lipid‐based systems by the …
been around for nearly two decades. Originally developed for lipid‐based systems by the …
Pragmatic coarse-graining of proteins: models and applications
The molecular details involved in the folding, dynamics, organization, and interaction of
proteins with other molecules are often difficult to assess by experimental techniques …
proteins with other molecules are often difficult to assess by experimental techniques …
The SIRAH force field: a suite for simulations of complex biological systems at the coarse-grained and multiscale levels
The different combinations of molecular dynamics simulations with coarse-grained
representations have acquired considerable popularity among the scientific community …
representations have acquired considerable popularity among the scientific community …
Application of computational approaches in biomembranes: From structure to function
Biological membranes (biomembranes) are one of the most complicated structures that
allow life to exist. Investigating their structure, dynamics, and function is crucial for advancing …
allow life to exist. Investigating their structure, dynamics, and function is crucial for advancing …
SPICA force field for proteins and peptides
A coarse-grained (CG) model for peptides and proteins was developed as an extension of
the Surface Property fItting Coarse grAined (SPICA) force field (FF). The model was …
the Surface Property fItting Coarse grAined (SPICA) force field (FF). The model was …
Specific interactions of peripheral membrane proteins with lipids: what can molecular simulations show us?
Peripheral membrane proteins (PMPs) can reversibly and specifically bind to biological
membranes to carry out functions such as cell signalling, enzymatic activity, or membrane …
membranes to carry out functions such as cell signalling, enzymatic activity, or membrane …
The role of transmembrane proteins in plant growth, development, and stress responses
Y Zhou, B Wang, F Yuan - International Journal of Molecular Sciences, 2022 - mdpi.com
Transmembrane proteins participate in various physiological activities in plants, including
signal transduction, substance transport, and energy conversion. Although more than 20 …
signal transduction, substance transport, and energy conversion. Although more than 20 …
Capturing choline–aromatics cation− π interactions in the MARTINI force field
Cation− π interactions play an important role in biomolecular recognition, including
interactions between membrane phosphatidylcholine lipids and aromatic amino acids of …
interactions between membrane phosphatidylcholine lipids and aromatic amino acids of …
A data-driven dimensionality reduction approach to compare and classify lipid force fields
Molecular dynamics simulations of all-atom and coarse-grained lipid bilayer models are
increasingly used to obtain useful insights for understanding the structural dynamics of these …
increasingly used to obtain useful insights for understanding the structural dynamics of these …
LipIDens: simulation assisted interpretation of lipid densities in cryo-EM structures of membrane proteins
Cryo-electron microscopy (cryo-EM) enables the determination of membrane protein
structures in native-like environments. Characterising how membrane proteins interact with …
structures in native-like environments. Characterising how membrane proteins interact with …