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

Emre Brookes, Borries Demeler, Mattia Rocco

Research output: Contribution to journalArticlepeer-review

Abstract

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. (Figure Presented)

Original languageEnglish
Pages (from-to)746-753
Number of pages8
JournalMacromolecular Bioscience
Volume10
Issue number7
DOIs
Publication statusPublished - Jul 7 2010

Keywords

  • Biopolymers
  • Computer modeling
  • Molecular dynamics
  • Structure-property relationships
  • Ultracentrifugation

ASJC Scopus subject areas

  • Biotechnology
  • Bioengineering
  • Biomaterials
  • Polymers and Plastics
  • Materials Chemistry

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