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

ABSTRACT: 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 sim

SUBMITTER: Blow KE 

PROVIDER: S-EPMC12648654 | biostudies-literature | 2025 Nov

REPOSITORIES: biostudies-literature