CCD2MD: A Suite of Packages for Preparing Co-Folded Outputs for Molecular Dynamics Simulations.

Protein-lipid interactions play a crucial role in the stability and function of membrane proteins. While experimental approaches to characterize these interactions in a native-like membrane environment can be challenging, computational techniques offer a powerful alternative for identifying and analyzing potential binding sites. Recent advances in cofolding methods now enable the prediction of holo protein structures, capturing conformational changes that may occur upon lipid binding and thereby improving the accuracy of binding site characterization. However, the outputs from these methods often require postprocessing to ensure compatibility with widely used molecular dynamics force fields. In this work, we introduce CCD2MD, a modular toolkit designed to convert cofolding outputs into simulation-ready systems for GROMACS. CCD2MD supports both atomistic and coarse-grained representations with or without membrane embedding. While CCD2MD is exemplified here with protein-lipid systems, its modular design allows for straightforward adaptation to other cofolded biomolecular assemblies, incorporating complexes with nucleic acids, small molecules, carbohydrates, or metal ions, thereby enabling a variety of simulation setups across multiple scales.