MemProtMD: Automated Insertion of Membrane Protein Structures into Explicit Lipid Membranes. (Q42072255)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26073602%20AND%20SRC:MED&resulttype=core&format=json

17 February 2020

title

MemProtMD: Automated Insertion of Membrane Protein Structures into Explicit Lipid Membranes (English)

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17 February 2020

0 references

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1

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17 February 2020

Martin Caffrey

3

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17 February 2020

Elisabeth P Carpenter

4

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17 February 2020

Joanne L. Parker

5

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17 February 2020

Simon Newstead

6

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17 February 2020

Mark S.P. Sansom

7

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17 February 2020

author name string

Joseph E Goose

2

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17 February 2020

publication date

11 June 2015

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17 February 2020

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17 February 2020

volume

23

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17 February 2020

issue

7

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17 February 2020

page(s)

1350-1361

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GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

17 February 2020

cites work

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X-ray structure of a calcium-activated TMEM16 lipid scramblase

5 June 2018

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Lipid clustering correlates with membrane curvature as revealed by molecular simulations of complex lipid bilayers

5 June 2018

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Mechanisms of integral membrane protein insertion and folding

5 June 2018

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Comparing crystal structures of Ca(2+) -ATPase in the presence of different lipids

5 June 2018

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A conformational landscape for alginate secretion across the outer membrane ofPseudomonas aeruginosa

5 June 2018

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Structural basis for outer membrane lipopolysaccharide insertion

5 June 2018

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Structure and mechanism of an intramembrane liponucleotide synthetase central for phospholipid biosynthesis

5 June 2018

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Structure-guided simulations illuminate the mechanism of ATP transport through VDAC1

5 June 2018

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Single particle electron cryo-microscopy of a mammalian ion channel

5 June 2018

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Molecular basis of nitrate uptake by the plant nitrate transporter NRT1.1

5 June 2018

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Crystal structure of the plant dual-affinity nitrate transporter NRT1.1

5 June 2018

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Structures of yeast mitochondrial ADP/ATP carriers support a domain-based alternating-access transport mechanism

5 June 2018

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Refined structures of mouse P-glycoprotein

5 June 2018

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Membrane protein orientation and refinement using a knowledge-based statistical potential

5 June 2018

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Helical membrane protein conformations and their environment

5 June 2018

1 reference

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Structures of P-glycoprotein reveal its conformational flexibility and an epitope on the nucleotide-binding domain

5 June 2018

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Structural adaptations of proteins to different biological membranes.

5 June 2018

1 reference

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X-ray structure of the mammalian GIRK2–βγ G-protein complex

5 June 2018

1 reference

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Structures of ABCB10, a human ATP-binding cassette transporter in apo- and nucleotide-bound states

5 June 2018

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Perspective on the Martini model.

5 June 2018

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Crystal structure of the integral membrane diacylglycerol kinase

5 June 2018

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Multiscale simulations reveal conserved patterns of lipid interactions with aquaporins.

5 June 2018

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The structural basis of ZMPSTE24-dependent laminopathies

5 June 2018

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Structural model for the protein-translocating element of the twin-arginine transport system

5 June 2018

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The cost of living in the membrane: a case study of hydrophobic mismatch for the multi-segment protein LeuT.

5 June 2018

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Simulation-based prediction of phosphatidylinositol 4,5-bisphosphate binding to an ion channel.

5 June 2018

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PDBTM: Protein Data Bank of transmembrane proteins after 8 years

5 June 2018

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Structure of the TatC core of the twin-arginine protein transport system

5 June 2018

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Crystal structure of the multidrug transporter P-glycoprotein from Caenorhabditis elegans

5 June 2018

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β-Barrel mobility underlies closure of the voltage-dependent anion channel

5 June 2018

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Structural determinants of the supramolecular organization of G protein-coupled receptors in bilayers.

5 June 2018

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Accurate de novo structure prediction of large transmembrane protein domains using fragment-assembly and correlated mutation analysis

5 June 2018

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5 June 2018

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OPM database and PPM web server: resources for positioning of proteins in membranes

5 June 2018

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Biological membranes: the importance of molecular detail

5 June 2018

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Side-chain hydrophobicity scale derived from transmembrane protein folding into lipid bilayers

5 June 2018

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5 June 2018

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Functional dynamics in the voltage-dependent anion channel

5 June 2018

1 reference

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MEDELLER: homology-based coordinate generation for membrane proteins

5 June 2018

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Principles of membrane protein interactions with annular lipids deduced from aquaporin-0 2D crystals

5 June 2018

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PIP(2)-binding site in Kir channels: definition by multiscale biomolecular simulations.

5 June 2018

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Biophysical dissection of membrane proteins.

5 June 2018

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Structure of the human voltage-dependent anion channel

5 June 2018

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OCTOPUS: improving topology prediction by two-track ANN-based preference scores and an extended topological grammar

5 June 2018

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Coarse-grained MD simulations of membrane protein-bilayer self-assembly.

5 June 2018

1 reference

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Fast procedure for reconstruction of full-atom protein models from reduced representations.

5 June 2018

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GPCR engineering yields high-resolution structural insights into beta2-adrenergic receptor function

5 June 2018

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Inference of macromolecular assemblies from crystalline state

5 June 2018

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PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations

5 June 2018

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Structure of a bacterial multidrug ABC transporter

5 June 2018

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Insertion and assembly of membrane proteins via simulation.

5 June 2018

1 reference

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The distribution of positively charged residues in bacterial inner membrane proteins correlates with the trans-membrane topology

5 June 2018

1 reference

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ABC lipid transporters: extruders, flippases, or flopless activators?

5 June 2018

1 reference

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Multipass membrane protein structure prediction using Rosetta

5 June 2018

1 reference

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Lipids in membrane protein structures

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4509712

Structure of mitochondrial ADP/ATP carrier in complex with carboxyatractyloside

5 June 2018

1 reference

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Ca2+ -ATPase structure in the E1 and E2 conformations: mechanism, helix-helix and helix-lipid interactions

5 June 2018

1 reference

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How proteins adapt to a membrane-water interface

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4509712

Internal packing of helical membrane proteins

5 June 2018

1 reference

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The GxxxG motif: a framework for transmembrane helix-helix association

5 June 2018

1 reference

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5 June 2018

The Protein Data Bank

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Comparative protein modelling by satisfaction of spatial restraints

5 June 2018

1 reference

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Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features

5 June 2018

1 reference

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The MARTINI Coarse-Grained Force Field: Extension to Proteins.

5 June 2018

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Lipid organization of the plasma membrane

17 August 2018

1 reference

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Structure-based statistical analysis of transmembrane helices.

17 August 2018

1 reference

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Electroporation of the E. coli and S. Aureus membranes: molecular dynamics simulations of complex bacterial membranes.

17 August 2018

1 reference

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Neurotransmitter/sodium symporter orthologue LeuT has a single high-affinity substrate site

17 August 2018

1 reference

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The voltage-dependent anion channel-1 modulates apoptotic cell death.

17 August 2018

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Escherichia coli diacylglycerol kinase is an evolutionarily optimized membrane enzyme and catalyzes direct phosphoryl transfer.

17 August 2018

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From Coarse Grained to Atomistic: A Serial Multiscale Approach to Membrane Protein Simulations

17 August 2018

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12 December 2020

Alteration of Na(+)-coupled transport in site-directed mutants of the melibiose carrier of Escherichia coli

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12 December 2020

Non-random distribution of amino acids in the transmembrane segments of human type I single span membrane proteins

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12 December 2020

Evidence for cardiolipin binding sites on the membrane-exposed surface of the cytochrome bc1

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12 December 2020

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Identifiers

DOI

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26073602%20AND%20SRC:MED&resulttype=core&format=json

17 February 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26073602%20AND%20SRC:MED&resulttype=core&format=json

17 February 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26073602%20AND%20SRC:MED&resulttype=core&format=json