Accessible Molecular Surface, Relative to Vaccum


The accessible molecular surface is calculated, relative to what the accessibility would be in vacuum. See chapter 9 of the WHAT IF writeup.


The accessibility is calculated twice. Once just normal for the protein you submitted to the server, and once for every residue with the conformation it has in the molecule, but all the rest of the molecule except the backbone of its two direct neighbours (if available) removed.
The accessible molecular surface calculated by WHAT IF comes within 5% of the well known Connolly surface area; the difference being that WHAT IF does not take the so-called reentrant surface into account. The surface is reported in squared Ångstroms. WHAT IF uses the following Van der Waals radii: C:1.8 Ångstrom; O:1.4 Ångstrom; N:1.7 Ångstrom; S:2.0 Ångstrom.
Either Choose a pdb-file,
Or Choose your own file

If you have detected any error, or have any question or suggestion, please send an Email to Gert Vriend.
Roland Krause, Maarten L Hekkelman, Jens E Nielsen, Gert Vriend.

Last modified Mon Jan 29 12:33:00 2018