[Chimera-users] surface hydrophobicity display

Tom Goddard goddard at sonic.net
Mon Jan 31 11:02:31 PST 2011

Hi Elaine,

   Occurs to me that if the electric field strength, ie the gradient of 
the electrostatic potential, is a useful measure similar to 
hydrophobicity, that can be viewed currently in Chimera with the surface 
color dialog using color by "volume data gradient norm".  You would need 
the electrostatic potential calculated for instance by APBS or DelPhi.


> Hi Sumitro,
> I did a little more digging for related information and thought I would share -- however, none of these methods are available in Chimera currently.
> ...  If I understood it correctly, they looked at how successfully Coulombic electrostatic potential and the gradient in that potential can be used to identify hydrophobic areas of surface (areas that bind hydrophobic atoms in the ligand).  Both were somewhat successful, but even better was a simple definition of hydrophobic surface as the part of the surface that is not close to hydrogen-bonding groups.  This paper is fairly old and the data set of ligand/receptor structures small.
> Elaine

More information about the Chimera-users mailing list