CellSys: An open-source tool for building initial structures for bio-membranes and drug-delivery systems

J Comput Chem. 2022 Feb 15;43(5):331-339. doi: 10.1002/jcc.26793. Epub 2021 Dec 13.

Abstract

Since phospholipids are the most important components in the structure of biomembranes, they deserve to be considered with a lot of attention in both experimental and computational theoretical studies using molecular simulation methods related to the research in the fields of drug design and drug delivery where they involve knowledge about the interactions of drug molecules with cell membranes. To employ the molecular simulation approach for this purpose the essential requirement is having information about the initial structure of phospholipids and how they interact with the drugs. Therefore in this article, we introduce an open-source software package in Python programming language for utilizing data manipulation for generation and developing the initial structure of biomolecular cells to provide the needed information for investigation in drug delivery systems. In addition, the proposed software package can be used for the efficient storage of membrane structural data to be exploited in designing new drug delivery systems. To verify the performance of the code and the results of the simulations, several analyses have been done, such as the calculation of area per lipid and self-diffusion coefficient, in addition to lipid order parameter. The results were in complete agreement with the references.

Keywords: cell membranes; molecular dynamics simulations; phospholipid membranes; python programming language.

MeSH terms

  • Cell Membrane / chemistry*
  • Drug Delivery Systems*
  • Molecular Dynamics Simulation
  • Phospholipids / chemistry*
  • Software*

Substances

  • Phospholipids