Dynamic Maintenance of Molecular Surfaces under Conformational Changes
Eran Eyal and Dan Halperin
We present an efficient algorithm for maintaining the boundary and surface area of
protein molecules as they undergo conformational changes. We also describe a robust im-
plementation of the algorithm and report on experimental results with our implementation
on proteins with hundreds of residues. Our work extends and combines two previous re-
sults: (i) controlled perturbation for static molecular surfaces , and (ii) data structures
for self-collision testing and energy maintenance of proteins that change conformation .
As our method keeps an exact representation of the boundary surface and of the voids in
the molecule, it can be useful in various applications such as Monte Carlo Simulation or
Molecular Dynamics Simulation. In addition we propose and analyze an alternative method
for efficiently recalculating the surface area under conformational (and hence topological)
changes based on techniques for efficient dynamic maintenance of graph connectivity.
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