Final Presentation - December 13, 2002
By Parag Jain
MASKER
- Masker is Christopher Bystroff's version of LeGrand and Merz's program [LeGrand, Merz 1993] of the same name that used Boolean masks to compute a solvent accessible surface (SAS) -- an expanded van der Waals surface.
- The Boolean masks approach for computing the SAS (first proposed by LeGrand and Merz) can be explained as under:
- A set of points were evenly spaced on the surface of a sphere centered at the origin and having radius 1.0, and each was represented by a single bit in a multi-byte word.
- A set of 'masks' was created by placing a probe sphere of unit radius at all positions around the origin, and all distances from zero to two.
- Points within the probe radius had their bits set to zero, while the remaining bits were set to one. Therefore, one multi-byte word (mask) corresponded to one probe sphere location.
- A binary AND operation over any number of masks resulted in another mask whose nonzero bits represent the SAS for one atom. The SAS is estimated quickly and accurately by summing the 1-bits and scaling.
- Bystroff's improved MASKER takes the method of LeGrand and Merz one step further by using masks to calculate SES:
- The contact surface is a scalar multiple of SAS.
- The toroidal surface is estimated based on the length of exposed circular edge at the intersection of two atom surfaces.
- The reentrant surface is calculated by placing a mask at each position where a probe is in contact with exactly three atoms.
- Intersections and self-burial of toroidal and reentrant surfaces are accounted for by additional masking operations, as are the pairwise partial derivatives.
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