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Coarse-grained protein models and their applications
The traditional computational modeling of protein structure, dynamics, and interactions
remains difficult for many protein systems. It is mostly due to the size of protein …
remains difficult for many protein systems. It is mostly due to the size of protein …
Perspective on the Martini model
The Martini model, a coarse-grained force field for biomolecular simulations, has found a
broad range of applications since its release a decade ago. Based on a building block …
broad range of applications since its release a decade ago. Based on a building block …
On develo** coarse-grained models for biomolecular simulation: a review
So-called coarse-grained models are a popular type of model for accessing long time scales
in simulations of biomolecular processes. Such models are coarse-grained with respect to …
in simulations of biomolecular processes. Such models are coarse-grained with respect to …
Modeling and simulation of ion channels
Transport of ions through pores in membranes is a process of fundamental importance to
cell biology. In living organisms, such transport is facilitated by ion channels that utilize the …
cell biology. In living organisms, such transport is facilitated by ion channels that utilize the …
From coarse grained to atomistic: a serial multiscale approach to membrane protein simulations
Coarse-grained molecular dynamics provides a means for simulating the assembly and the
interactions of membrane protein/lipid complexes at a reduced level of representation …
interactions of membrane protein/lipid complexes at a reduced level of representation …
The role of cholesterol in M2 clustering and viral budding explained
The influenza A M2 homotetrameric channel consists of four transmembrane (TM) and four
amphipathic helices (AHs). This viral proton channel is suggested to form clusters in the …
amphipathic helices (AHs). This viral proton channel is suggested to form clusters in the …
Hybrid simulations: combining atomistic and coarse-grained force fields using virtual sites
Hybrid simulations, in which part of the system is represented at atomic resolution and the
remaining part at a reduced, coarse-grained, level offer a powerful way to combine the …
remaining part at a reduced, coarse-grained, level offer a powerful way to combine the …
Reconstruction of atomistic details from coarse‐grained structures
We present an algorithm to reconstruct atomistic structures from their corresponding coarse‐
grained (CG) representations and its implementation into the freely available molecular …
grained (CG) representations and its implementation into the freely available molecular …
A massively parallel infrastructure for adaptive multiscale simulations: modeling RAS initiation pathway for cancer
Computational models can define the functional dynamics of complex systems in
exceptional detail. However, many modeling studies face seemingly incommensurate …
exceptional detail. However, many modeling studies face seemingly incommensurate …
Structure and Mechanism of the Influenza A M218–60 Dimer of Dimers
We report a magic angle spinning (MAS) NMR structure of the drug-resistant S31N mutation
of M218–60 from Influenza A. The protein was dispersed in diphytanoyl-sn-glycero-3 …
of M218–60 from Influenza A. The protein was dispersed in diphytanoyl-sn-glycero-3 …