Sphere-packings, lattices, and groups
Sphere-packings, lattices, and groups
Linear clustering of objects with multiple attributes
SIGMOD '90 Proceedings of the 1990 ACM SIGMOD international conference on Management of data
Introduction to parallel computing: design and analysis of algorithms
Introduction to parallel computing: design and analysis of algorithms
Dynamic Partitioning of Non-Uniform Structured Workloads with Spacefilling Curves
IEEE Transactions on Parallel and Distributed Systems
Analysis of the clustering properties of Hilbert space-filling curve
Analysis of the clustering properties of Hilbert space-filling curve
Parallel programming with MPI
RECOMB '97 Proceedings of the first annual international conference on Computational molecular biology
Parallel Algorithms in Molecular Biology
HPCN Europe '97 Proceedings of the International Conference and Exhibition on High-Performance Computing and Networking
Parallel remapping algorithms for adaptive problems
FRONTIERS '95 Proceedings of the Fifth Symposium on the Frontiers of Massively Parallel Computation (Frontiers'95)
Many-to-many personalized communication with bounded traffic
FRONTIERS '95 Proceedings of the Fifth Symposium on the Frontiers of Massively Parallel Computation (Frontiers'95)
Dynamic Load Balancing Schemes for Computing Accessible Surface Area of Protein Molecules
HIPC '98 Proceedings of the Fifth International Conference on High Performance Computing
A Provably Optimal, Distribution-Independent Parallel Fast Multipole Method
IPDPS '00 Proceedings of the 14th International Symposium on Parallel and Distributed Processing
Parallel Domain Decomposition and Load Balancing Using Space-Filling Curves
HIPC '97 Proceedings of the Fourth International Conference on High-Performance Computing
Independent component analysis algorithms for microarray data analysis
Intelligent Data Analysis - Knowledge Discovery in Bioinformatics
ICCSA'05 Proceedings of the 2005 international conference on Computational Science and its Applications - Volume Part I
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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 O(n), where n is the number of atoms in the protein molecule. For computing sphere intersections, we present hash-based algorithms that run in O(n) expected sequential time and O\left({n\over p}\right) expected parallel time and sort-based algorithms that run in worst-case O\left(n\log n\right) sequential time and O\left({n\log n\over p}\right) parallel time. These are significant improvements over previously known algorithms which take O\left(n^2\right) time sequentially and O\left(\frac{n^2}{p}\right) 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.