Please tell me what kind of model to build
PACE achieves accurate descriptions of protein–lipid interactions through systematic parameterization. The interaction parameters between protein particles and the hydrophobic tails of lipids are fitted based on the solvation free energies of small molecules in hexadecane, while those between protein particles and lipid polar headgroups are optimized according to the potentials of mean force obtained from all-atom simulations. This enables PACE to correctly reproduce the insertion orientation, stability, and aggregation behavior of membrane peptides and membrane proteins.
The PACE Membrane Builder supports rapid construction of membrane protein or peptide systems in a coarse-grained membrane environment. This module also allows the creation of hybrid-resolution models, enabling users to retain atomic-level details for selected protein regions. Users can upload PDB files or specify a PDB ID to download structures from OPM or RCSB, automatically generating initial conformations embedded in lipid membranes, with flexible options for membrane type and solvation conditions. It is also compatible with PACE mix.