Dynamic maintenance of molecular surfaces under conformational changes

Eran Eyal*, Dan Halperin

*Corresponding author for this work

Research output: Contribution to conferencePaperpeer-review


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 [26]. As our method keeps a highly accurate 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; initial results of the implementation of this method show great promise.

Original languageEnglish
Number of pages10
StatePublished - 2005
Event21st Annual Symposium on Computational Geometry, SCG'05 - Pisa, Italy
Duration: 6 Jun 20058 Jun 2005


Conference21st Annual Symposium on Computational Geometry, SCG'05


  • Controlled Perturbation
  • Dynamic Data Structures
  • Molecular Simulations
  • Molecular Surfaces
  • Robust Geometric Computing


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