Membrane protein structure quality in molecular dynamics simulation.

Membrane protein structure quality in molecular dynamics simulation.

Our goal was to assess the relationship between membrane protein quality, output from protein quality checkers and output from molecular dynamics (MD) simulations. Membrane transport proteins are essential for a wide range of cellular processes. Structural features of integral membrane proteins are...

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Bibliografische gegevens
Hoofdauteurs:	Law, R, Capener, C, Baaden, M, Bond, P, Campbell, J, Patargias, G, Arinaminpathy, Y, Sansom, MS
Formaat:	Conference item
Gepubliceerd in:	2005

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Molecular dynamics simulations of GlpF in a micelle vs in a bilayer: conformational dynamics of a membrane protein as a function of environment.
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Conformational sampling and dynamics of membrane proteins from 10-nanosecond computer simulations.
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OmpT: molecular dynamics simulations of an outer membrane enzyme.
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Molecular dynamics simulations and membrane protein structure quality.
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OmpT: Molecular dynamics simulations of an outer membrane enzyme.
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Outer membrane proteins: comparing X-ray and NMR structures by MD simulations in lipid bilayers.
door: Cox, K, et al.
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Molecular dynamics simulations of outer membrane phospholipase A
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Molecular dynamics simulations exploring the KcsA structure
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Interdomain dynamics and ligand binding: molecular dynamics simulations of glutamine binding protein.
door: Pang, A, et al.
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Membrane proteins: molecular dynamics simulations.
door: Lindahl, E, et al.
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Molecular dynamics simulations of a K channel model: Sensitivity to changes in ions, waters, and membrane environment
door: Capener, C, et al.
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Coarse-grained molecular dynamics simulations of membrane proteins and peptides.
door: Bond, P, et al.
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Ion channels: structural bioinformatics and modelling.
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Molecular Dynamics simulations of spontaneous micelle formation around membrane proteins.
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A molecular dynamics investigation of mono and dimeric states of the outer membrane enzyme OMPLA.
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Coarse-grain simulations of the R-SNARE fusion protein in its membrane environment detect long-lived conformational sub-states.
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Simulations of bacterial outer membrane proteins: Towards an e-outer membrane
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Molecular dynamics simulations of the ligand-binding domain of the ionotropic glutamate receptor GluR2.
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Self-assembly of a simple membrane protein: coarse-grained molecular dynamics simulations of the influenza M2 channel.
door: Carpenter, T, et al.
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The simulation approach to bacterial outer membrane proteins.
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Insertion and assembly of membrane proteins via simulation.
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Membrane protein dynamics versus environment: simulations of OmpA in a micelle and in a bilayer.
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Molecular simulation approaches to membrane proteins.
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Membrane protein simulations: ion channels and bacterial outer membrane proteins.
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Homology modelling and molecular dynamics simulations of a prokaryotic glutamate receptor: GluR0
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One membrane protein, two structures and six environments: a comparative molecular dynamics simulation study of the bacterial outer membrane protein PagP.
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Molecular simulations and lipid-protein interactions: potassium channels and other membrane proteins.
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Molecular dynamics simulations of membrane proteins.
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A prokaryotic glutamate receptor: homology modelling and molecular dynamics simulations of GluR0.
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BioSimGRID: Application to analysis of membrane protein simulations
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Comparative molecular dynamics simulations: Glutamate receptors and periplasmic binding proteins
door: Sansom, M, et al.
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Extending the structure of an ABC transporter to atomic resolution: modeling and simulation studies of MsbA.
door: Campbell, J, et al.
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Structure and dynamics of K channel pore-lining helices: a comparative simulation study.
door: Shrivastava, I, et al.
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Simulation studies of the interactions between membrane proteins and detergents.
door: Bond, P, et al.
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Binding site flexibility: molecular simulation of partial and full agonists within a glutamate receptor.
door: Arinaminpathy, Y, et al.
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CGDB: a database of membrane protein/lipid interactions by coarse-grained molecular dynamics simulations.
door: Chetwynd, A, et al.
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Conformational dynamics of OmpA: MD simulations of a bacterial outer membrane protein
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A brief history of visualizing membrane systems in molecular dynamics simulations
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OmpA: gating and dynamics via molecular dynamics simulations.
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Homology modeling and molecular dynamics simulation studies of an inward rectifier potassium channel.
door: Capener, C, et al.
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