CHARMM-GUI Membrane Builder statistics

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CHARMM-GUI Membrane Builder specifications


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 in publications

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 […]

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 […]

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 […]

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 […]

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 . […]

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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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