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.
Brookes
Emre
E
Department of Biochemistry, The University of Texas Health Science Center at San Antonio, San Antonio, Texas, TX 78229, USA.
Demeler
Borries
B
Rocco
Mattia
M
D000465:Algorithms; D000596:Amino Acids / Q000032:analysis; D006801:Humans; D046911:Macromolecular Substances / Q000737:chemistry*; D008863:Microspheres; D008958:Models, Molecular; D012996:Solutions / Q000737:chemistry*; D013499:Surface Properties; D014461:Ultracentrifugation / Q000379:methods*
D000596:Amino Acids; D046911:Macromolecular Substances; D012996:Solutions