Protocol to study the oligomeric organization of single-span transmembrane peptides using molecular dynamics simulations.

Herein, you will find detailed information for the preparation of a coarse-grained array of peptides embedded in a lipid membrane. It contains all the steps to set up and run a molecular dynamic simulation using a coarse-grained approach. We provide analytical tools and scripts for generating a residue-level contact matrix between multiple peptides, as well as geometric analysis of arrangements between multiple peptides. This protocol was designed to study the organization of transmembrane peptides in an unbiased manner using computational approaches. For complete details on the use and execution of this protocol, please refer to Smulski et al. (2022).