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Measuring Properties of Molecular Surfaces Using Ray Casting

Mike Phillips, Iliyan Georgiev, Anna Katharina Dehof, Stefan Nickels, Lukas Marsalek, Hans-Peter Lenhof, Philipp Slusallek, and Andreas Hildebrandt

Proceedings of 9th International Workshop on High Performance Computational Biology
Atlanta, April 2010

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Abstract

Molecular geometric properties, such as volume, exposed surface area, and occurrence of internal cavities, are important inputs to many applications in molecular modeling. In this work we describe a very general and highly efficient approach for the accurate computation of such properties, which is applicable to arbitrary molecular surface models. The technique relies on a high performance ray casting framework that can be easily adapted to the computation of further quantities of interest at interactive speed, even for huge models.