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

Macromol Biosci. 2010 Jul 7;10(7):746-53. doi: 10.1002/mabi.200900474.


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.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Algorithms*
  • Amino Acids / analysis
  • Humans
  • Macromolecular Substances / chemistry*
  • Microspheres*
  • Models, Molecular*
  • Solutions / chemistry*
  • Surface Properties
  • Ultracentrifugation / methods*


  • Amino Acids
  • Macromolecular Substances
  • Solutions