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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 …
Molecular dynamics simulation of an entire cell
The ultimate microscope, directed at a cell, would reveal the dynamics of all the cell's
components with atomic resolution. In contrast to their real-world counterparts …
components with atomic resolution. In contrast to their real-world counterparts …
Membrane lipids drive formation of KRAS4b-RAF1 RBDCRD nanoclusters on the membrane
The oncogene RAS, extensively studied for decades, presents persistent gaps in
understanding, hindering the development of effective therapeutic strategies due to a lack of …
understanding, hindering the development of effective therapeutic strategies due to a lack of …
Machine learning-driven multiscale modeling: bridging the scales with a next-generation simulation infrastructure
Interdependence across time and length scales is common in biology, where atomic
interactions can impact larger-scale phenomenon. Such dependence is especially true for a …
interactions can impact larger-scale phenomenon. Such dependence is especially true for a …
Facilitating CG simulations with MAD: The MArtini database server
The MArtini Database (MAD-https://mad. ibcp. fr) is a web server designed for the sharing of
structures and topologies of molecules parametrized with the Martini coarse-grained (CG) …
structures and topologies of molecules parametrized with the Martini coarse-grained (CG) …
Machine learning–driven multiscale modeling reveals lipid-dependent dynamics of RAS signaling proteins
RAS is a signaling protein associated with the cell membrane that is mutated in up to 30% of
human cancers. RAS signaling has been proposed to be regulated by dynamic …
human cancers. RAS signaling has been proposed to be regulated by dynamic …
[HTML][HTML] Classical molecular dynamics
This issue of JCP highlights both developments in and applications of classical molecular
simulation in 67 articles. A recent issue of JCP focused on electronic structure software …
simulation in 67 articles. A recent issue of JCP focused on electronic structure software …
An implementation of the Martini coarse-grained force field in OpenMM
We describe a complete implementation of Martini 2 and Martini 3 in the OpenMM molecular
dynamics software package. Martini is a widely used coarse-grained force field with …
dynamics software package. Martini is a widely used coarse-grained force field with …
Generalizable coordination of large multiscale workflows: challenges and learnings at scale
The advancement of machine learning techniques and the heterogeneous architectures of
most current supercomputers are propelling the demand for large multiscale simulations that …
most current supercomputers are propelling the demand for large multiscale simulations that …