Improved Maintenance of Molecular Surfaces Using Dynamic Graph Connectivity
- Cite this paper as:
- Eyal E., Halperin D. (2005) Improved Maintenance of Molecular Surfaces Using Dynamic Graph Connectivity. In: Casadio R., Myers G. (eds) Algorithms in Bioinformatics. WABI 2005. Lecture Notes in Computer Science, vol 3692. Springer, Berlin, Heidelberg
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  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.
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