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MemBuilder specifications


Unique identifier OMICS_08568
Name MemBuilder
Interface Web user interface
Restrictions to use None
Computer skills Basic
Version 2.0
Stability Beta
Maintained Yes


  • person_outline Seyed Shahriar Arab

Publication for MemBuilder

MemBuilder citations


Binding Modes of Teixobactin to Lipid II: Molecular Dynamics Study

Sci Rep
PMCID: 5722933
PMID: 29222455
DOI: 10.1038/s41598-017-17606-5

[…] velocities.After the TXB-LII complex was stabilized in the aqueous simulations, we checked the stability of the complex in a membrane environment. The membrane model was built utilizing a web server MemBuilder II and parameterized with a Slipids force field published by Jambeck and Lyubertsev–, which is compatible with AMBER force field. In the prepared lipid bilayer, each leaflet of the membrane […]


Micelle Maker: An Online Tool for Generating Equilibrated Micelles as Direct Input for Molecular Dynamics Simulations

PMCID: 5579539
PMID: 28884160
DOI: 10.1021/acsomega.7b00820

[…] ructures, avoiding a modeler’s frustration with error-prone models and equilibration issues.We note here as an aside two more tools of value when generating micelles. The first is an extension to the MemBuilder server (MemBuilder II,, which was originally developed to build lipid bilayers but has now also been extended to build micelles and liposomes. The […]


Membrane Mediated Antimicrobial and Antitumor Activity of Cathelicidin 6: Structural Insights from Molecular Dynamics Simulation on Multi Microsecond Scale

PLoS One
PMCID: 4938549
PMID: 27391304
DOI: 10.1371/journal.pone.0158702

[…] ural properties in the absence of lipid membrane environments in AMBER99SB-ILDN [] and CHARMM36 [] force fields for a time period of 0.5 μs. Anionic and zwitterionic lipid bilayers were created using MemBuilder [] program and were equilibrated prior to peptide addition. The equilibrated lipid bilayer systems were considered for peptide-lipid structural analysis using Slipid/AMBER and AMBER99SB-ILD […]


Binding of the Antagonist Caffeine to the Human Adenosine Receptor hA2AR in Nearly Physiological Conditions

PLoS One
PMCID: 4439127
PMID: 25992797
DOI: 10.1371/journal.pone.0126833

[…] Membrane models in systems I, II and III were generated using the MemBuilder tool []. The inflateGRO code [] was used to pack lipids around the hA2AR constructed in the previous step. The systems were inserted in a simulation box of size 14.8 nm x 11.1 nm x 10.0 nm. […]


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MemBuilder institution(s)
Department of Biophysics, School of Biological Sciences, Tarbiat Modares University, Tehran, Iran
MemBuilder funding source(s)
This research was in part supported by a grant from Biomath Research group at IPM.

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