Viewing Geometric Protein Structures From Inside a CAVE
IEEE Computer Graphics and Applications
Computational Biology and Chemistry
Power diagrams and intersection detection
ICCSA'11 Proceedings of the 2011 international conference on Computational science and its applications - Volume Part III
Interactive extraction and tracking of biomolecular surface features
EuroVis '13 Proceedings of the 15th Eurographics Conference on Visualization
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Common geometric models for proteins and other molecules are the space filling diagram, the solvent accessible surface, and the molecular surface. We describe software that computes metric properties of these models, including volume and surface area. It also measures voids or empty space enclosed by the protein, and it keeps track of surface area contributions of individual atoms. The software is based on 3-dimensional alpha complexes and on inclusion-exclusion formulas with terms derived from the simplices in this complex.