Get area buried#

Querying average buried surface area per residue upon protein folding.

The function molsysmt.physchem.get_area_buried() extracts tabulated values (in Å²) representing average area buried upon folding using reference experimental scales (Rose et al.).

Added in version 1.0.0.

API documentation

Follow this link for a detailed description of the input arguments, raised errors, and returned objects of this function: molsysmt.physchem.get_area_buried().

Basic usage#

Let’s retrieve the average buried area per residue for a protein structure:

import molsysmt as msm

molsys = msm.convert(msm.systems['Trp-Cage']['1l2y.h5msm'])

Note

Demo Systems Catalog

This tutorial uses demonstration datasets provided by MolSysMT. To explore the full catalog of bundled systems, forms, and file paths, visit the Demo Systems guide.

We query the tabulated buried area values using the Rose scale:

ab = msm.physchem.get_area_buried(molsys, element='group', definition='rose')
print('Average buried area (Rose, Å^2):\n', ab)

Average buried area (Rose, Å^2):
 [103.3 164.1 177.7 158.  119.2 224.6 164.1 115.5  97.8  62.9  62.9  92.9
  85.6  85.6  62.9 162.2  92.9  92.9  92.9  85.6]