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
- 7 July 2010
- journal article
- research article
- Published by Wiley in Macromolecular Bioscience
- Vol. 10 (7), 746-753
- https://doi.org/10.1002/mabi.200900474
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.Keywords
Funding Information
- National Institutes of Health (RR022200)
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