PISA reports ASA/BSA on residue level as well. Internally, it keeps
information on atomic level
(including ASA/BSA "per atom"), but the atom-level output was never done.
The reason is,
I could never imagine that such level of description has any good meaning.
"Surface area" is
an abstraction for _m
Daniel Bonsor wrote:
I am trying to calculate the contact surface area of a loop. Using ArealMol
I only get the overall contact surface area per residue. Is there any way to
get it per atom or does anyone know of a program (online/software) which
will perform this task.
Thanks in advance
Dan
Hi Dan-
There's an online server and program called DPX which will calculate the
depth of all the atoms in your PDB file. An atom's depth is defined as the
minimum distance it is to the nearest solvent accessible atom, with depth =
0 meaning the atom is not buried at all (most likely at the protein
Sorry I should of made this clearer in my original post. Thanks anyway to
people who have responded thus far.
I am trying to calculate the buried surface area of a loop which folds from
a disordered to an ordered state.
I am looking for a program that will allow me to calculate;
(1) the buried s
I am trying to calculate the contact surface area of a loop. Using ArealMol
I only get the overall contact surface area per residue. Is there any way to
get it per atom or does anyone know of a program (online/software) which
will perform this task.
Thanks in advance
Dan
Daniel A. Bonsor,
Bost
