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MERMAID: dedicated web server to prepare and run coarse-grained membrane protein dynamics.

ABSTRACT: Atomistic molecular dynamics simulations of membrane proteins have been shown to be extremely useful for characterizing the molecular features underlying their function, but require high computational power, limiting the understanding of complex events in membrane proteins, e.g. ion channels gating, GPCRs activation. To overcome this issue, it has been shown that coarse-grained approaches, although requiring less computational power, are still capable of correctly describing molecular events underlying big conformational changes in biological systems. Here, we present the Martini coarse-grained membrane protein dynamics (MERMAID), a publicly available web interface that allows the user to prepare and run coarse-grained molecular dynamics (CGMD) simulations and to analyse the trajectories.

SUBMITTER: Damre M

PROVIDER: S-EPMC6602572 | biostudies-literature | 2019 Jul

REPOSITORIES: biostudies-literature

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MERMAID: dedicated web server to prepare and run coarse-grained membrane protein dynamics.

Damre Mangesh M Marchetto Alessandro A Giorgetti Alejandro A

Nucleic acids research 20190701 W1

Atomistic molecular dynamics simulations of membrane proteins have been shown to be extremely useful for characterizing the molecular features underlying their function, but require high computational power, limiting the understanding of complex events in membrane proteins, e.g. ion channels gating, GPCRs activation. To overcome this issue, it has been shown that coarse-grained approaches, although requiring less computational power, are still capable of correctly describing molecular events und ...[more]

PMID: 31106328

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