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Issue No.06 - June (2002 vol.13)

pp: 544-555

ABSTRACT

<p>We present faster sequential and parallel algorithms for computing the solvent accessible surface area (ASA) of protein molecules. The ASA is computed by finding the exposed surface areas of the spheres obtained by increasing the van der Waals radii of the atoms with the van der Waals radius of the solvent. Using domain specific knowledge, we show that the number of sphere intersections is only <tmath>O(n)</tmath>, where <tmath>n</tmath> is the number of atoms in the protein molecule. For computing sphere intersections, we present hash-based algorithms that run in <tmath>O(n)</tmath> expected sequential time and <tmath>O\left({n\over p}\right)</tmath> expected parallel time and sort-based algorithms that run in worst-case <tmath>O\left(n\log n\right)</tmath> sequential time and <tmath>O\left({n\log n\over p}\right)</tmath> parallel time. These are significant improvements over previously known algorithms which take <tmath>O\left(n^2\right)</tmath> time sequentially and <tmath>O\left(\frac{n^2}{p}\right)</tmath> time in parallel. We present a Monte Carlo algorithm for computing the solvent accessible surface area. The basic idea is to generate points uniformly at random on the surface of spheres obtained by increasing the van der Waals radii of the atoms with the van der Waals radius of the solvent molecule and to test the points for accessibility. We also provide error bounds as a function of the sample size. Experimental verification of the algorithms is carried out using an IBM SP-2.</p>

INDEX TERMS

Computational biology, accessible surface area, protein folding, parallel algorithm, Monte Carlo.

CITATION

Natsuhiko Futamura, Srinivas Aluru, Desh Ranjan, Bhanu Hariharan, "Efficient Parallel Algorithms for Solvent Accessible Surface Area of Proteins",

*IEEE Transactions on Parallel & Distributed Systems*, vol.13, no. 6, pp. 544-555, June 2002, doi:10.1109/TPDS.2002.1011399