Rapid approximation to molecular surface area via the use of Boolean logic and look-up tables
Journal of Computational Chemistry
Sparsification—a technique for speeding up dynamic graph algorithms
Journal of the ACM (JACM)
A perturbation scheme for spherical arrangements with application to molecular modeling
Computational Geometry: Theory and Applications - special issue on applied computational geometry
Spheres, molecules, and hidden surface removal
Computational Geometry: Theory and Applications
Randomized fully dynamic graph algorithms with polylogarithmic time per operation
Journal of the ACM (JACM)
Near-optimal fully-dynamic graph connectivity
STOC '00 Proceedings of the thirty-second annual ACM symposium on Theory of computing
SODA '01 Proceedings of the twelfth annual ACM-SIAM symposium on Discrete algorithms
Digital Principles and Applications
Digital Principles and Applications
Computing Smooth Molecular Surfaces
IEEE Computer Graphics and Applications
Dynamic maintenance and visualization of molecular surfaces
Discrete Applied Mathematics - Special issue: Computational molecular biology series issue IV
An Experimental Study of Polylogarithmic, Fully Dynamic, Connectivity Algorithms
Journal of Experimental Algorithmics (JEA)
An Experimental Study of Polylogarithmic, Fully Dynamic, Connectivity Algorithms
Journal of Experimental Algorithmics (JEA)
Dynamic maintenance of molecular surfaces under conformational changes
SCG '05 Proceedings of the twenty-first annual symposium on Computational geometry
A dynamic data structure for flexible molecular maintenance and informatics
2009 SIAM/ACM Joint Conference on Geometric and Physical Modeling
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We present recent developments in efficiently maintaining the boundary and surface area of protein molecules as they undergo conformational changes. As the method that we devised keeps a highly accurate representation of the outer boundary surface and of the voids in the molecule, it can be useful in various applications, in particular in Monte Carlo Simulation. The current work continues and extends our previous work [10] and implements an efficient method for recalculating the surface area under conformational (and hence topological) changes based on techniques for efficient dynamic maintenance of graph connectivity. This method greatly improves the running time of our algorithm on most inputs, as we demonstrate in the experiments reported here.