Solvent-accessible surface fraction of atoms?

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?





Cheers!


Dragos

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?





Regards,


Miklos