What are pockets and
Pockets are empty concavities on a protein surface into which solvent (probe sphere
1.4 A) can gain access, i.e., these concavities have mouth openings connecting
their interior with the outside bulk solution. Currently, shallow depressions
are excluded from the calculation. A technical definition to distinguish a pocket
from a shallow depression is the following: among the infinite number of possible
cross sections of a pocket, at least one is larger than the mouth opening of the
A cavity (or void) is an interior empty space that is not accessible to the solvent
probe. It has no mouth openings to the outside bulk solution.
Computational Geometry: Voronoi Diagram, Delaunay Triangulation,
and Alpha Shape
CASTp is based on recent theorectical and algorithmic results of Computational
Geometry. It has many advantages: 1) pockets and cavities are identified analytically,
2) the boundary between the bulk solvent and the pocket is defined precisely,
3) all calculated parameters are rotationally invariant, and do not involve discretization
and they make no use of dot surface or grid points.
The following contains excerpts from Liang et al, 1998.
The basic ingredients of Computational Geometry applied in CASTp are: Delaunay
triangulation, alpha shape, and discrete flow (Edelsbrunner & Mucke 1994; Edelsbrunner
1995; Facello 1995; Edelsbrunner & Shah 1996; Edelsbrunner et al, 1998). Consider
a highly simplified hypothetical model, a two dimensional molecule formed by atom
disks, all of the same radius (Figure 1a). If nails are figuratively hammered
into the plane at each atom center, and a rubber band is stretched around the
entire collection of nails, the band encloses a convex hull of the molecule,
containing all atom centers within. The convex hull of the disk centers in Figure
1a is the shape enclosed by the outer boundary of the polygon in Figure 1b (shaded
area). It can be triangulated, i.e., tessellated with triangles so that there
is neither a missing piece, nor overlap, of the triangles. Triangulation of a
convex hull is shown in Figure 1b, where triangles tile all of the shaded convex
hull area. This particular triangulation, called the Delaunay triangulation,
is especially useful because it is mathematically equivalent to another geomectric
construct, the Voronoi diagram (the pattern formed by all dashed lines
in Figure 1a).
The Voronoi diagram is formed by the collection of Voronoi cells. For the hypothetical
molecule in Figure 1a, Voronoi cells include the convex polygons bounded all around
by dashed lines, as well as the polygons with edges defined by dashed lines, but
extending to infinity. Each cell contains on atom, and those extending to infinity
contain boundary atoms of the convex hull. A Voronoi cell consists of the space
around one atom so that the distance of every spatial point in the cell to its
atom is less than or equal to the distance to any other atom of the molecule.
The Delaunay triangulation can be mapped from the Voronoi diagram directly. Across
every Voronoi edge seperating two neighboring Voronoi cells, a line segment connecting
the corresponding two atom centers is placed. For every Voronoi vertex where three
Voronoi cells intersect, a triangle who's vertices are the three atom centers
is placed. In this way, the full Delaunay triangulation is obtained by mapping
from the Voronoi diagram. That is, both the Delaunay triangulation and the Voronoi
diagram contain equivalent information.
To obtain the alpha shape, or dual complex, the mapping process
is repeated, except that the Voronoi edges and vertices completely outside the
molecule are omitted. Figure 1c shows the dual complex for the 2-d molecule in
Figure 1a. The edges of the Delaunay triangulation corresponding to the omitted
Voronoi edges are the dotted edges in Figure 1c; a triangle with one or more dotted
edges is designated an "empty" triangle (though not all empty triangles have dotted
edges). The dual complex and the Delaunay triangulation are two key constructs
that are reich in geometric information; from them the area and volume of the
molecule, and of the interior inaccessible cavities, can be measured. As an example,
a void at the bottom center in the dual complex (Figure 1c) is easily identified
as a collection of empty triangles (3 in this case) for which the enclosing polygon
has solid edges. There is a one-to-one correspondence between such a void in the
dual complex, and an inaccessible cavity in the molecule. The actual size of the
molecular cavity can be obtained by subtracting from the sum of the areas of the
triangles, the fractions of the atom disks contained within the triangle. Details
for computing cavity area and volume are in (Edelsbrunner et al, 1995; Liang et
For identifying and measuring pockets, the discrete flow method is employed.
For the 2-D model, discrete flow is defined only for empty triangles, that is,
those Delaunay triangles that are not part of the dual complex. An obtuse
empty triangle "flows" to its neighboring triangle, whereas an acute empty triangle
is a sink that collects flow from neighboring empty triangles. Figure 2a
shows a pocket formed by five empty Delaunay triangles. Obtuse triangles 1,4,
and 5 flow to the sink, triangle 2. Triangle 3 is also obtuse; it flows to triangle
4, and continues to flow to triangle 2. All flows are stored, and empty triangles
are later merged when they share dotted edges (dual, non-complex edges). Ultimately,
the pocket is delineated as a collection of empty triangles. The actual size of
the molecular pocket is computed by subtracting the fractions of atom disks contained
within each empty triangle. The 2-D mouth is the dotted edge on the boundary
of the pocket (upper edge of triangle 1, in this case), minus the two radii of
the atoms connected by the edge. The type of surface depression not identified
as a pocket is illustrated in Figure 2b; it is one formed by five obtuse triangles
that flow sequentially from 1 to 5 to the outside, or infinity.
All the features of the 2-D description have more complex 3-D counterparts.
The convex hull in three dimensions is a convex polytope instead of a polygon,
and its Delaunay triangulation is a tessellation of the polytope with tetrahedra.
When atoms have different radii, the weighted Delaunay triangulation
is required, and the corresponding weighted Voronoi cells are also different
- Edelsbrunner H, Mucke EP. 1994. Three-dimensional alpha shapes.
ACM Trans. Graphics 13:43-72.
- Edelsbrunner H. 1995. The union of balls and its dual shape.
Discrete Comput. Geom. 13:415-440.
- Edelsbrunner H, Shah NR. 1996. Incremental topological flipping works for regular triangulations. Algorithmica 15:223-241.
- Edelsbrunner H, Facello M, Fu P, Liang J. 1995. Measuring proteins and voids in proteins. In: Proc. 28th Ann. Hawaii Int'l Conf.
System Sciences. Los Alamitos, California: IEEE Computer Society
Press. pp. 256-264.
- Edelsbrunner H, Facello M, Liang J. 1998. On the definition and the
construction of pockets in macromolecules. Disc. Appl. Math.
- Facello MA. 1995. Implementation of a randomized algorihtm for
Delaunay and regular triangulations in three dimensions. Computer
Aided Geometric Design. 12:349-370.
- Liang J, Edelsbrunner H, Woodward C. 1998. Anatomy of protein
pockets and caviteis: measurement of binding site geometry and implications
for ligand design. Protein Science. 7:1884-1897.
- J. Liang, H. Edelsbrunner, P. Fu, P.V. Sudhakar and S. Subramaniam. 1998.
Analytical shape computing of
macromolecules I: molecular area and volume through alpha shape.
Proteins. 33, 1-17.
- Liang J, Edelsbrunner H, Fu P, Sudhakar PV, Subramaniam S. 1998b.
Analytical shape computation of macromolecules. II. Identification and
computation of inaccessible cavities in proteins. Proteins: Struct.
Funct. Genet. 33:18-29.
|Please note: For various reasons the CASTp calculation cannot be performed on certain protein structures.
While this is only true for approximately 1% of the PDB, we apologize for any inconviences. Here is a list of known structures in that fall in this category.