Rapid approximation to molecular surface area via the use of Boolean logic and look-up tables
Journal of Computational Chemistry
Fast and robust computation of molecular surfaces
Proceedings of the eleventh annual symposium on Computational geometry
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
Controlled perturbation for arrangements of polyhedral surfaces with application to swept volumes
SCG '99 Proceedings of the fifteenth annual symposium on Computational geometry
Randomized fully dynamic graph algorithms with polylogarithmic time per operation
Journal of the ACM (JACM)
Introduction to Robotics: Mechanics and Control
Introduction to Robotics: Mechanics and Control
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
Algorithms exploiting the chain structure of proteins
Algorithms exploiting the chain structure of proteins
Controlled perturbation for Delaunay triangulations
SODA '05 Proceedings of the sixteenth annual ACM-SIAM symposium on Discrete algorithms
Design of the CGAL 3D Spherical Kernel and application to arrangements of circles on a sphere
Computational Geometry: Theory and Applications
Computing the arrangement of circles on a sphere, with applications in structural biology
Computational Geometry: Theory and Applications
A dynamic data structure for flexible molecular maintenance and informatics
2009 SIAM/ACM Joint Conference on Geometric and Physical Modeling
Kernel modeling for molecular surfaces using a uniform solution
Computer-Aided Design
Topologies of surfaces on molecules and their computation in O(n) time
Computer-Aided Design
Controlled perturbation for certified geometric computing with fixed-precision arithmetic
ICMS'10 Proceedings of the Third international congress conference on Mathematical software
Improved maintenance of molecular surfaces using dynamic graph connectivity
WABI'05 Proceedings of the 5th International conference on Algorithms in Bioinformatics
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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.