Sciweavers

COMPGEOM
2005
ACM

Dynamic maintenance of molecular surfaces under conformational changes

14 years 28 days ago
Dynamic maintenance of molecular surfaces under conformational changes
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 implementation of the algorithm and report on experimental results with our implementation on proteins with hundreds of residues. Our work extends and combines two previous results: (i) controlled perturbation for static molecular surfaces [18], and (ii) data structures for self-collision testing and energy maintenance of proteins that change conformation [25]. As our method keeps an exact combinatorial 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. Categories a...
Eran Eyal, Dan Halperin
Added 13 Oct 2010
Updated 13 Oct 2010
Type Conference
Year 2005
Where COMPGEOM
Authors Eran Eyal, Dan Halperin
Comments (0)