Table 1

A list of each feature contained within our surface descriptor
Feature # Name Description
1 % Visibility Percentage of outside world visible from point
2 Non-Polar Backbone Distance to the nearest Non-Polar Backbone Atom
3 Arom. Sidechain Distance to the nearest Aromatic Sidechain Atom
4 Aliph. Sidechain Distance to the nearest Aliphatic Sidechain Atom
5 N Backbone Distance to the nearest Nitrogen Backbone Atom
6 O Backbone Distance to the nearest Oxygen Backbone Atom
7 S Backbone Distance to the nearest Sulpher Sidechain Atom
8 Amide N Sidechain Distance to the nearest Amide Nitrogen Sidechain Atom
9 Amide O Sidechain Distance to the nearest Amide Oxygen Sidechain Atom
10 Trp Sidechain Distance to the nearest Trypophan Sidechain Atom
11 Hydroxyl Sidechain Distance to the nearest Hydroxyl Sidechain Atom
12 Charged O Sidechain Distance to the nearest Charged Oxygen Sidechain Atom
13 Charged N Sidechain Distance to the nearest Charged Nitrogen Sidechain Atom
14 Anisotropy (1.6 Å) Patch anisotropy, with radius: 1.6 Å
15 Anisotropy (3.2 Å) Patch anisotropy, with radius: 3.2 Å
16 Anisotropy (4.8 Å) Patch anisotropy, with radius: 4.8 Å
17 Anisotropy (6.4 Å) Patch anisotropy, with radius: 6.4 Å
18 Anisotropy (8 Å) Patch anisotropy, with radius: 8 Å
19 Curvature (1.6 Å) Patch curvature, with radius: 1.6 Å
20 Curvature (3.2 Å) Patch curvature, with radius: 3.2 Å
21 Curvature (4.8 Å) Patch curvature, with radius: 4.8 Å
22 Curvature (6.4 Å) Patch curvature, with radius: 6.4 Å
23 Curvature (8 Å) Patch curvature, with radius: 8 Å
24 Curvature Var. (1.6 Å) Variance of curvature within patch of radius: 1.6 Å
25 Curvature Var. (3.2 Å) Variance of curvature within patch of radius: 3.2 Å
26 Curvature Var. (4.8 Å) Variance of curvature within patch of radius: 4.8 Å
27 Curvature Var. (6.4 Å) Variance of curvature within patch of radius: 6.4 Å
28 Curvature Var. (8 Å) Variance of curvature within patch of radius: 8 Å
29 Hydropathy (1.6 Å) Weighted avg. hydropathy over patch of radius: 1.6 Å
30 Hydropathy (3.2 Å) Weighted avg. hydropathy over patch of radius: 3.2 Å
31 Hydropathy (4.8 Å) Weighted avg. hydropathy over patch of radius: 4.8 Å
32 Hydropathy (6.4 Å) Weighted avg. hydropathy over patch of radius: 6.4 Å
33 Hydropathy (8 Å) Weighted avg. hydropathy over patch of radius: 8 Å
34 Charge (1.6 Å) Weighted avg. charge over patch of radius: 1.6 Å
35 Charge (3.2 Å) Weighted avg. charge over patch of radius: 3.2 Å
36 Charge (4.8 Å) Weighted avg. charge over patch of radius: 4.8 Å
37 Charge (6.4 Å) Weighted avg. charge over patch of radius: 6.4 Å
38 Charge (8 Å) Weighted avg. charge over patch of radius: 8 Å
39 Hyd. Bond Donor Distance to nearest potential external hydrogen bond donor
40 Hyd. Bond Acceptor Distance to nearest potential external hydrogen bond acceptor

Note that features 14 - 38 are weighted according to distance (from center vertex) and point area (i.e. the sum of the areas of all adjacent triangles).

Cipriano et al.

Cipriano et al. BMC Bioinformatics 2012 13:314   doi:10.1186/1471-2105-13-314

Open Data