Solvent-accessible surface fraction of atoms?

User 21b7e0228c

14-12-2005 09:21:39

Hi there,

Do you happen to have any quick (& dirty) means to estimate the fraction of solvent-accessible area of EACH ATOM in a molecule (based on topology or geometry, either way's fine as far as it's reasonably accurate). Since you have a TPSA predictor, there may be a way to get access to each of the atoms that make up the mol?



ChemAxon efa1591b5a

16-12-2005 12:27:06

Hi Dragos,

what we could possible use to estimate polar surface area of atoms is the Connolly surface calculation implemented in MarvinSpace. The surface is approximated by a triangle mesh, the precision can be set by parameters. The representation of the triangularized surface can identify atoms corresponding to each individual triangles. We can implement a fairly simple calculation that summarizes the areas of polar and non-polar triangles (ie. triangles corresponding to polar atoms).

Would this meet your needs?