Surface buried by a ligand.


This server calculates the molecular surface area that is buried because a ligand is bound to a macromolecule.


The accessible molecular surface area of the ligand and the macromolecule are calculated in the docked situation and after moving the ligand far outside the macromolecule. The difference is listed.
Use the List a file server in the server class Administration to find out what is the residue number of your ligand.
Peptides, nucleotides or sugars are not acceptable as ligands in the server version of this WHAT IF option. The program can use such ligands in interactive mode.
Help is available for residue numbers and for residue input.
Either Choose a pdb-file,
Or Choose your own file
Enter ligand molecule number

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