Developments in the US-SOMO Bead Modeling Suite: New Features in the Direct Residue-to-Bead Method, Improved Grid Routines, and Influence of Accessible Surface Area Screening

The US‐SOMO suite provides a flexible interface for accurately computing solution parameters from 3D structures of biomacromolecules through bead‐modeling approaches. We present an extended analysis of the influence of accessible surface area screening, overlap reduction routines, and approximations for non‐coded residues and missing atoms on the computed parameters for models built by the residue‐to‐bead direct correspondence and the cubic grid methods. Importantly, by taking the theoretical hydration into account at the atomic level, the performance of the grid‐type models becomes comparable or exceeds that of the corresponding hydrated residue‐to‐bead models. The UltraScan US‐SOMO suite is a powerful collection of algorithms for computing macromolecular hydrodynamics from 3D atomic structures through bead modeling procedures. The accuracy of the results and their dependence on various settings, like overlap removal procedures and hydration schemes, are thoroughly investigated in this paper.