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CHARMM-GUI Membrane Builder specifications

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Unique identifier OMICS_08570
Name CHARMM-GUI Membrane Builder
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Publications for CHARMM-GUI Membrane Builder

CHARMM-GUI Membrane Builder citations

 (37)
library_books

Identification and characterization of smallest pore forming protein in the cell wall of pathogenic Corynebacterium urealyticum DSM 7109

2018
BMC Biochem
PMCID: 5944148
PMID: 29743008
DOI: 10.1186/s12858-018-0093-9

[…] the particle mesh ewald algorithm []. lennard-jones potentials were computed using the 10–12 å force-switch scheme. the systems were equilibrated for 16 ns following the protocol described in the charmm-gui membrane builder []. unbiased production runs of 500 ns each were performed for the two systems in the pressure ensemble. the nosé-hoover thermostat [] was used to maintain a constant […]

library_books

Substrate bound outward open structure of a Na+ coupled sialic acid symporter reveals a new Na+ site

2018
Nat Commun
PMCID: 5931594
PMID: 29717135
DOI: 10.1038/s41467-018-04045-7

[…] v2.0.2. next, the transporter was inserted in each of the 8 states described in supplementary table  into a 1-palmitolyl-2-oleoyl-sn-glycero-3-phosphatidylethanolamine (pope) membrane using the charmm-gui membrane builder. each system was then solvated in a rectangular box (90 × 90 × 106 å3) containing 150 mm na+ and cl− resulting in final system sizes of ~86,000 atoms. all system files […]

library_books

Mechanistic insights into allosteric regulation of the A2A adenosine G protein coupled receptor by physiological cations

2018
Nat Commun
PMCID: 5893540
PMID: 29636462
DOI: 10.1038/s41467-018-03314-9

[…] this end, a configuration of a 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (popc) bilayer with 200 (2ydo simulations) or 166 (3qak and 5g53 simulations) lipids per leaflet was obtained from the charmm-gui membrane builder, solvated with 80 water molecules per lipid, energy minimized, and simulated for 300 ns. a snapshot was extracted at a random time between 50 and 300 ns, translated […]

library_books

Homology modeling and docking studies of a Δ9 fatty acid desaturase from a Cold tolerant Pseudomonas sp. AMS8

2018
PeerJ
PMCID: 5863719
PMID: 29576935
DOI: 10.7717/peerj.4347

[…] the model structure of the δ9-fatty acid desaturase was simulated in an embedded 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (popc) bilayer. the protein-bilayer system was constructed using charmm-gui membrane builder (). the atomistic md simulations were performed using charmm36 force field () in gromacs version 5 () within an integration time step of 20 fs. the simulation temperature […]

library_books

Structure and electrical properties of DNA nanotubes embedded in lipid bilayer membranes

2017
Nucleic Acids Res
PMCID: 5861442
PMID: 29136243
DOI: 10.1093/nar/gkx1078

[…] zwitterionic phospholipid with two asymmetric hydrocarbon chains, p and o, attached to phosphatialdylcholines (pcs). we generated the initial configuration of the popc lipid bilayer membrane using charmm-gui membrane builder (). next, we created a pore in the membrane by removing all the lipid molecules within a radius of 3 nm from the center of the membrane as shown in top panel of in . […]

library_books

Identification of a Different Agonist Binding Site and Activation Mechanism of the Human P2Y1 Receptor

2017
Sci Rep
PMCID: 5653743
PMID: 29062134
DOI: 10.1038/s41598-017-14268-1

[…] and ser207 of ecl2 residues were added back by homology modelling using the modeller module of chimera, and residues ala203ecl2 and ala1864.51 were mutated back to threonine and isoleucine., the charmm-gui membrane builder was used to construct the membrane-lipid systems. the transmembrane helical bundle of p2y1r was oriented along the z-axis of the popc bilayer and the overlapping lipid […]


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CHARMM-GUI Membrane Builder institution(s)
Department of Biological Sciences and Bioengineering Program, Lehigh University, Bethlehem, PA, USA; Leadership Computing Facility, Argonne National Laboratory, Argonne, IL, USA; Department of Chemistry and the Biophysics Program, University of Michigan, Ann Arbor, MI, USA

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