Dear Raghda Abogabal

These papers might be useful, have a look:

1. https://www.sciencedirect.com/science/article/abs/pii/S0959440X96801217

2. https://pubmed.ncbi.nlm.nih.gov/8794167/

3. https://pubmed.ncbi.nlm.nih.gov/11772445/

4. https://www.hindawi.com/journals/jphar/2018/9285854/

5. https://onlinelibrary.wiley.com/doi/10.1002/cjoc.202000655?af=R

6. https://www.taylorfrancis.com/chapters/edit/10.3109/9781420078053-10/design-formulation-protein-based-npdds-satheesh-podaralla-radhey-kaushik-omathanu-perumal

7. https://www.dovepress.com/protein-corona-a-new-approach-for-nanomedicine-design-peer-reviewed-fulltext-article-IJN

8. https://pubs.rsc.org/en/content/articlelanding/2020/nr/c9nr08519j

9. https://www.frontiersin.org/articles/10.3389/fmolb.2020.607323/full

Kind Regards

Qamar Ul Islam

I need a program to design and calculate

What exactly do you need? To simply build up a lipid bilayer model, you can use MemGen ( http://memgen.uni-goettingen.de ). MemGen creates multi-component lipid bilayer membranes for molecular dynamics simulations.

LipidBuilder ( https://lipidbuilder.epfl.ch/home ) is another possibility:

The physicochemical properties of the different lipid species are essential for the structural and functional organization of the biological membrane and its interaction with integral and peripheral membrane proteins. The lipid head groups are not the only important determinants of membranes; the nature of the lipid acyl chains strongly influences membrane properties.

To facilitate the creation of realistic biological membranes for molecular simulations, the present web-server, based on a VMD plug-in and CHARMM force field, allows creating, storing and sharing lipid libraries.

HTMD Membrane Builder ( https://software.acellera.com/docs/latest/htmd/tutorials/MembraneBuilder.html )- Making membrane building easy

Molecular dynamics simulations can be used to study biological membranes or even systems of proteins embedded in membranes. Such examples include the well-known GPCR proteins which are of high medical interest. Setting up a membrane simulation however can be quite challenging as they require tightly-packed pre-equilibrated membranes of different lipid compositions of different dimensions which are not always readily available.

Tools such as CHARMM-GUI already exist which provide the functionality for creating such membranes with great flexibility, they cannot however be used programmatically or in a batch manner.

HTMD provides a membrane builder tool which can be used to easily and quickly create a bilayer lipid membrane with a single command.

Another tool which might be of use to you is the CHARMM-GUI Membrane Builder for Complex Biological Membrane Simulations with Glycolipids and Lipoglycans

( https://pureadmin.qub.ac.uk/ws/portalfiles/portal/162126285/mbuilder_revised.pdf )

To get the orientation of Proteins in the lipid bilayer, you might want to look at the OPM database. Orientations of Proteins in Membranes (OPM) database (https://opm.phar.umich.edu) OPM provides spatial arrangements of membrane proteins with respect to the hydrocarbon core of the lipid bilayer.