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Relative Surface exposure.


Introduction

Often normal accessibility calculations exaggerate things. This server calculates for every residue what its accessibility would be if you would have mutated it into an alanine.

Methods

All residues are one after the other temporarily mutated into alanine, and the accessibility of that alanine is calculated and tabulated. No structural corrections or energy minimisations are made to compensate for the mutation.
Either Choose a pdb-file,
Or Choose your own file

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.

The accessible molecular surface is calculated using the WHAT IF method as described in chapter 9 of the WHAT IF writeup. 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