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MemBuilder: a web-based graphical interface to build heterogeneously mixed membrane bilayers for the GROMACS

Mohammad Mehdi Ghahremanpour¹, Seyed Shahriar Arab, Saman Biook Aghazadeh

¹Department of Bioinformatics, School of Computer Science, Institute for Research in Fundamental Sciences (IPM), Tehran, Iran, Department of Biophysics, School of Biological Sciences, Tarbiat Modares University, Tehran, Iran, School of Mathematics, Institute for Research in Fundamental Sciences (IPM), Tehran, Iran, Department of Computer Science, Faculty of Engineering, University of Tehran, Tehran, Iran, Department of Cell and Molecular Biology, Uppsala University, SE-75124 Uppsala, Sweden and Department of Chemistry, Zhejiang University, Hangzhou 310027, China.

Bioinformatics (Oxford, England)

|November 26, 2013

Summary

MemBuilder simplifies creating realistic multi-component lipid bilayers for molecular dynamics simulations. This web tool generates complex membrane models, improving the accuracy of simulations for membrane proteins.

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Area of Science:

Biophysics
Computational Biology

Background:

Molecular dynamics (MD) simulations are crucial for studying membrane proteins.
Current MD membrane models lack realism, often containing only one lipid type.
Realistic lipid composition and distribution are vital for membrane protein function.

Purpose of the Study:

To develop a tool for automated construction of heterogeneous lipid bilayers.
To provide molecular topologies for lipids compatible with united and all-atom force fields.

Main Methods:

Developed MemBuilder, a web-based graphical user interface.
MemBuilder automates the building process of complex lipid membranes.

Main Results:

MemBuilder simplifies the creation of realistic multi-component lipid bilayers.
The tool supports both united and all-atom force fields for molecular topologies.

Conclusions:

MemBuilder enhances the accuracy of MD simulations by enabling realistic membrane models.
This tool facilitates research on membrane proteins and lipid-protein interactions.