Final Presentation - December 13, 2002
By Parag Jain
Methods
Here we describe the calculations required to estimate the SES given a set of atomic coordinates, v, and radii, r, including the probe radius rw.
- Generation of the template and indexing of masks:
- 4096 points were placed randomly on a unit sphere.
- A mask is defined as a set of points on a sphere, bisected by a plane.
- Points on one side of the bisecting plane are set to zero, and the rest are set to 1.
- Each mask is represented as a 512-byte words (4096 bits).
- Estimating contact surface:
- The estimated contact surface for atom i is the number of 1-bits in atom_mask, times a scale factor.
- Here "#" denotes the number of 1-bits, out of 4096 possible.
- Estimating toroidal surface:
- The toroidal surface is calculated by the following equation:
- Estimating reentrant surface:
- The set of points where a water makes contact with exactly three atoms correspond to
a set of concave reentrant surfaces that are, in the simplest cases, spherical triangles of
radius rw.
- If there is a reentrant surface based on atoms i, j, and k, then its area is calculated by
placing a probe at vw, the vertex of a tetrahedron with sides (dij, dik, dkj, ri+rw, rj+rw,
rk+rw). A mask (probe_mask) is placed on that position. The reentrant surface area is:
- Implementation and availability:
- The MS calculation has been encoded as a Fortran90 module called MASKER,
linkable to Fortran programs as well as C.
- The input files are a library of masks, a table of mask index data,
an atom library, and the atomic coordinates in PDB format.
- The program outputs the SES and also a dot surface in PDB format for visualization
using molecular display programs, such as RasMol (Bystroff 2002, private conversation).
Next slide