JOY's default relative accessibility cut-off (7% or less) was used to define solvent inaccessible (buried) residues.
In the Pfu structure, conserved residues Arg288 and Arg292 of the α7 anchoring-helix are well defined and solvent exposed (Figures 3B and 6A) as in other structures of free full length Ffh (Ssol and Taq).
Users can define a solvent exclusion force or use the pairwise energy parameters considering the implicit solvent as an extra atom-type.
23 An ion exclusion layer (Stern layer) for the solvent ions was defined around the solvent-accessible surface using an ionic radius of 2 Å.
Bulk water molecules were then added with the Solvate program using a minimal water shell thickness of 6 Å and eight gaussians to define the solvent boundary.
This example from ref (426) indicates the importance of defining a solvent reactive coordinate that is "dedicated" to PT in describing PCET reactions and pertinent rate constants.
Inspired by the POCKET and SURFNET algorithms (Laskowski, 1995; Levitt and Banaszak, 1992), we define the solvent accessible surface by first checking for van der Waals clashes of protein atoms with a pseudo water molecule located at each grid point.
The dielectric boundary between the protein and the solvent was defined by calculating the solvent-accessible surface generated by a rolling probe sphere of 1.4 Å radius.
To obtain the molecular solvation free energy data for the two solvents, a proper potential energy function was defined for each solvent with respect to atomic distributions and three kinds of atomic parameters.
The size of the shortfall in the scheme – £571m, on one measure – means the Pension Protection Fund, which is funded by a levy on solvent defined benefit schemes, would still be on the hook for a very large sum.
Due to their heterogeneity and inherent complexity, the composition of extractives is largely defined by the solvent used for extraction such as ethanol-benzene, acetone, ethanol or water.
